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Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A. Extensive folding variability between homologous chromosomes in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.591087. [PMID: 38766012 PMCID: PMC11100664 DOI: 10.1101/2024.05.08.591087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
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2
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Wei J, Zhang W, Jiang A, Peng H, Zhang Q, Li Y, Bi J, Wang L, Liu P, Wang J, Ge Y, Zhang L, Yu H, Li L, Wang S, Leng L, Chen K, Dong B. Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids. Nat Commun 2024; 15:2395. [PMID: 38493164 PMCID: PMC10944513 DOI: 10.1038/s41467-024-46780-0] [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: 01/27/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Zygotic genome activation (ZGA) is a universal process in early embryogenesis of metazoan, when the quiescent zygotic nucleus initiates global transcription. However, the mechanisms related to massive genome activation and allele-specific expression (ASE) remain not well understood. Here, we develop hybrids from two deeply diverged (120 Mya) ascidian species to symmetrically document the dynamics of ZGA. We identify two coordinated ZGA waves represent early developmental and housekeeping gene reactivation, respectively. Single-cell RNA sequencing reveals that the major expression wave exhibits spatial heterogeneity and significantly correlates with cell fate. Moreover, allele-specific expression occurs in a species- rather than parent-related manner, demonstrating the divergence of cis-regulatory elements between the two species. These findings provide insights into ZGA in chordates.
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Affiliation(s)
- Jiankai Wei
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wei Zhang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - An Jiang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hongzhe Peng
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Yuting Li
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jianqing Bi
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Linting Wang
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Penghui Liu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jing Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yonghang Ge
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Liya Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Haiyan Yu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Lei Li
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shi Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119 Haibin Rd, Nansha Dist., Guangzhou, 511458, China.
| | - Bo Dong
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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3
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Hurabielle C, LaFlam TN, Gearing M, Ye CJ. Functional genomics in inborn errors of immunity. Immunol Rev 2024; 322:53-70. [PMID: 38329267 PMCID: PMC10950534 DOI: 10.1111/imr.13309] [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] [Indexed: 02/09/2024]
Abstract
Inborn errors of immunity (IEI) comprise a diverse spectrum of 485 disorders as recognized by the International Union of Immunological Societies Committee on Inborn Error of Immunity in 2022. While IEI are monogenic by definition, they illuminate various pathways involved in the pathogenesis of polygenic immune dysregulation as in autoimmune or autoinflammatory syndromes, or in more common infectious diseases that may not have a significant genetic basis. Rapid improvement in genomic technologies has been the main driver of the accelerated rate of discovery of IEI and has led to the development of innovative treatment strategies. In this review, we will explore various facets of IEI, delving into the distinctions between PIDD and PIRD. We will examine how Mendelian inheritance patterns contribute to these disorders and discuss advancements in functional genomics that aid in characterizing new IEI. Additionally, we will explore how emerging genomic tools help to characterize new IEI as well as how they are paving the way for innovative treatment approaches for managing and potentially curing these complex immune conditions.
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Affiliation(s)
- Charlotte Hurabielle
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Taylor N LaFlam
- Division of Pediatric Rheumatology, Department of Pediatrics, UCSF, San Francisco, California, USA
| | - Melissa Gearing
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, UCSF, San Francisco, California, USA
- Institute of Computational Health Sciences, UCSF, San Francisco, California, USA
- Gladstone Genomic Immunology Institute, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, UCSF, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, California, USA
- Arc Institute, Palo Alto, California, USA
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4
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Xu H, Zhang S, Duan Q, Lou M, Ling Y. Comprehensive analyses of 435 goat transcriptomes provides insight into male reproduction. Int J Biol Macromol 2024; 255:127942. [PMID: 37979751 DOI: 10.1016/j.ijbiomac.2023.127942] [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: 08/02/2023] [Revised: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
A systematic analysis of genes related to reproduction is crucial for obtaining a comprehensive understanding of the molecular mechanisms that underlie male reproductive traits in mammals. Here, we utilized 435 goat transcriptome datasets to unveil the testicular tissue-specific genes (TSGs), allele-specific expression (ASE) genes and their uncharacterized transcriptional features related to male goat reproduction. Results showed a total of 1790 TSGs were identified in goat testis, which was the most among all tissues. GO enrichment analyses suggested that testicular TSGs were mainly involved in spermatogenesis, multicellular organism development, spermatid development, and flagellated sperm motility. Subsequently, a total of 95 highly conserved TSGs (HCTSGs), 508 middle conserved TSGs (MCTSGs) and 42 no conserved TSGs (NCTSGs) were identified in goat testis. GO enrichment analyses suggested that the HCTSGs and MCTSGs has a more important association with male reproduction than NCTSGs. Additionally, we identified 644 ASE genes, including 88 tissue-specific ASE (TS-ASE) genes (e.g., FSIP2, TDRD9). GO enrichment analyses indicated that both ASE genes and TS-ASE genes were associated with goat male reproduction. Overall, this study revealed an extensive gene set involved in the regulation of male goat reproduction and their dynamic transcription patterns. Data reported here provide valuable insights for a further improvement of the economic benefits of goats as well as future treatments for male infertility.
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Affiliation(s)
- Han Xu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Sihuan Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Qin Duan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Mengyu Lou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, Anhui, China.
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5
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Lobanova YV, Zhenilo SV. Genomic Imprinting and Random Monoallelic Expression. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:84-96. [PMID: 38467547 DOI: 10.1134/s000629792401005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 03/13/2024]
Abstract
The review discusses the mechanisms of monoallelic expression, such as genomic imprinting, in which gene transcription depends on the parental origin of the allele, and random monoallelic transcription. Data on the regulation of gene activity in the imprinted regions are summarized with a particular focus on the areas controlling imprinting and factors influencing the variability of the imprintome. The prospects of studies of the monoallelic expression are discussed.
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Affiliation(s)
- Yaroslava V Lobanova
- Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Svetlana V Zhenilo
- Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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6
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Prowse-Wilkins CP, Wang J, Garner JB, Goddard ME, Chamberlain AJ. Allele specific binding of histone modifications and a transcription factor does not predict allele specific expression in correlated ChIP-seq peak-exon pairs. Sci Rep 2023; 13:15596. [PMID: 37730913 PMCID: PMC10511416 DOI: 10.1038/s41598-023-42637-6] [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: 12/03/2022] [Accepted: 09/13/2023] [Indexed: 09/22/2023] Open
Abstract
Allele specific expression (ASE) is widespread in many species including cows. Therefore, regulatory regions which control gene expression should show cis-regulatory variation which mirrors this differential expression within the animal. ChIP-seq peaks for histone modifications and transcription factors measure activity at functional regions and the height of some peaks have been shown to correlate across tissues with the expression of particular genes, suggesting these peaks are putative regulatory regions. In this study we identified ASE in the bovine genome in multiple tissues and investigated whether ChIP-seq peaks for four histone modifications and the transcription factor CTCF show allele specific binding (ASB) differences in the same tissues. We then investigate whether peak height and gene expression, which correlates across tissues, also correlates within the animal by investigating whether the direction of ASB in putative regulatory regions, mirrors that of the ASE in the genes they are putatively regulating. We found that ASE and ASB were widespread in the bovine genome but vary in extent between tissues. However, even when the height of a peak was positively correlated across tissues with expression of an exon, ASE of the exon and ASB of the peak were in the same direction only half the time. A likely explanation for this finding is that the correlations between peak height and exon expression do not indicate that the height of the peak causes the extent of exon expression, at least in some cases.
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Affiliation(s)
- Claire P Prowse-Wilkins
- Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia.
| | - Jianghui Wang
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia
| | - Josie B Garner
- Agriculture Victoria, Ellinbank Dairy Centre, Ellinbank, VIC, 3821, Australia
| | - Michael E Goddard
- Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, VIC, 3010, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia
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7
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Gao Z, Yang X, Chen J, Rausher MD, Shi T. Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation. PLANT PHYSIOLOGY 2023; 191:1662-1683. [PMID: 36417237 PMCID: PMC10022630 DOI: 10.1093/plphys/kiac522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Both cis- and trans-regulatory mutations drive changes in gene expression that underpin plant phenotypic evolution. However, how and why these two major types of regulatory mutations arise in different genes and how gene expression is inherited and associated with these regulatory changes are unclear. Here, by studying allele-specific expression in F1 hybrids of pink-flowered sacred lotus (Nelumbo nucifera) and yellow-flowered American lotus (N. lutea), we reveal the relative contributions of cis- and trans-regulatory changes to interspecific expression rewiring underlying petal color change and how the expression is inherited in hybrids. Although cis-only variants influenced slightly more genes, trans-only variants had a stronger impact on expression differences between species. In F1 hybrids, genes under cis-only and trans-only regulatory effects showed a propensity toward additive and dominant inheritance, respectively, whereas transgressive inheritance was observed in genes carrying both cis- and trans-variants acting in opposite directions. By investigating anthocyanin and carotenoid coexpression networks in petals, we found that the same category of regulatory mutations, particularly trans-variants, tend to rewire hub genes in coexpression modules underpinning flower color differentiation between species; we identified 45 known genes with cis- and trans-regulatory variants significantly correlated with flower coloration, such as ANTHOCYANIN 5-AROMATIC ACYLTRANSFERASE (ACT), GLUTATHIONE S-TRANSFERASE F11 (GSTF11), and LYCOPENE Ε-CYCLASE (LCYE). Notably, the relative abundance of genes in different categories of regulatory divergence was associated with the inferred magnitude of constraints like expression level and breadth. Overall, our study suggests distinct selective constraints and modes of gene expression inheritance among different regulatory mutations underlying lotus petal color divergence.
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Affiliation(s)
- Zhiyan Gao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan 430081, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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8
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Sleiman MB, Roy S, Gao AW, Sadler MC, von Alvensleben GVG, Li H, Sen S, Harrison DE, Nelson JF, Strong R, Miller RA, Kutalik Z, Williams RW, Auwerx J. Sex- and age-dependent genetics of longevity in a heterogeneous mouse population. Science 2022; 377:eabo3191. [PMID: 36173858 PMCID: PMC9905652 DOI: 10.1126/science.abo3191] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DNA variants that modulate life span provide insight into determinants of health, disease, and aging. Through analyses in the UM-HET3 mice of the Interventions Testing Program (ITP), we detected a sex-independent quantitative trait locus (QTL) on chromosome 12 and identified sex-specific QTLs, some of which we detected only in older mice. Similar relations between life history and longevity were uncovered in mice and humans, underscoring the importance of early access to nutrients and early growth. We identified common age- and sex-specific genetic effects on gene expression that we integrated with model organism and human data to create a hypothesis-building interactive resource of prioritized longevity and body weight genes. Finally, we validated Hipk1, Ddost, Hspg2, Fgd6, and Pdk1 as conserved longevity genes using Caenorhabditis elegans life-span experiments.
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Affiliation(s)
- Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center (UTHSC), Memphis, TN 38163, USA
| | - Arwen W. Gao
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Marie C. Sadler
- Institute of Primary Care and Public Health (Unisante), University of Lausanne, Lausanne 1011, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Giacomo V. G. von Alvensleben
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Hao Li
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | | | - James F. Nelson
- Barshop Center for Longevity Studies at the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Randy Strong
- Barshop Center for Longevity Studies at the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- South Texas Veterans Healthcare System, San Antonio, TX 78229, USA
| | - Richard A. Miller
- Department of Pathology, University of Michigan Geriatrics Center, Ann Arbor, MI 48109-2200, USA
| | - Zoltán Kutalik
- Institute of Primary Care and Public Health (Unisante), University of Lausanne, Lausanne 1011, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center (UTHSC), Memphis, TN 38163, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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9
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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10
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Barreto VM, Kubasova N, Alves-Pereira CF, Gendrel AV. X-Chromosome Inactivation and Autosomal Random Monoallelic Expression as "Faux Amis". Front Cell Dev Biol 2021; 9:740937. [PMID: 34631717 PMCID: PMC8495168 DOI: 10.3389/fcell.2021.740937] [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: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 12/23/2022] Open
Abstract
X-chromosome inactivation (XCI) and random monoallelic expression of autosomal genes (RMAE) are two paradigms of gene expression regulation where, at the single cell level, genes can be expressed from either the maternal or paternal alleles. X-chromosome inactivation takes place in female marsupial and placental mammals, while RMAE has been described in mammals and also other species. Although the outcome of both processes results in random monoallelic expression and mosaicism at the cellular level, there are many important differences. We provide here a brief sketch of the history behind the discovery of XCI and RMAE. Moreover, we review some of the distinctive features of these two phenomena, with respect to when in development they are established, their roles in dosage compensation and cellular phenotypic diversity, and the molecular mechanisms underlying their initiation and stability.
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Affiliation(s)
- Vasco M Barreto
- Chronic Diseases Research Centre, CEDOC, Nova Medical School, Lisbon, Portugal
| | - Nadiya Kubasova
- Chronic Diseases Research Centre, CEDOC, Nova Medical School, Lisbon, Portugal
| | - Clara F Alves-Pereira
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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11
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Abstract
Diploidy has profound implications for population genetics and susceptibility to genetic diseases. Although two copies are present for most genes in the human genome, they are not necessarily both active or active at the same level in a given individual. Genomic imprinting, resulting in exclusive or biased expression in favor of the allele of paternal or maternal origin, is now believed to affect hundreds of human genes. A far greater number of genes display unequal expression of gene copies due to cis-acting genetic variants that perturb gene expression. The availability of data generated by RNA sequencing applied to large numbers of individuals and tissue types has generated unprecedented opportunities to assess the contribution of genetic variation to allelic imbalance in gene expression. Here we review the insights gained through the analysis of these data about the extent of the genetic contribution to allelic expression imbalance, the tools and statistical models for gene expression imbalance, and what the results obtained reveal about the contribution of genetic variants that alter gene expression to complex human diseases and phenotypes.
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Affiliation(s)
- Siobhan Cleary
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway H91 H3CY, Ireland;
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12
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Zhao Q, Kong Y, Kittredge A, Li Y, Shen Y, Zhang Y, Tsang SH, Yang T. Distinct expression requirements and rescue strategies for BEST1 loss- and gain-of-function mutations. eLife 2021; 10:67622. [PMID: 34061021 PMCID: PMC8169119 DOI: 10.7554/elife.67622] [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] [Received: 02/19/2021] [Accepted: 05/10/2021] [Indexed: 01/23/2023] Open
Abstract
Genetic mutation of the human BEST1 gene, which encodes a Ca2+-activated Cl- channel (BEST1) predominantly expressed in retinal pigment epithelium (RPE), causes a spectrum of retinal degenerative disorders commonly known as bestrophinopathies. Previously, we showed that BEST1 plays an indispensable role in generating Ca2+-dependent Cl- currents in human RPE cells, and the deficiency of BEST1 function in patient-derived RPE is rescuable by gene augmentation (Li et al., 2017). Here, we report that BEST1 patient-derived loss-of-function and gain-of-function mutations require different mutant to wild-type (WT) molecule ratios for phenotypic manifestation, underlying their distinct epigenetic requirements in bestrophinopathy development, and suggesting that some of the previously classified autosomal dominant mutations actually behave in a dominant-negative manner. Importantly, the strong dominant effect of BEST1 gain-of-function mutations prohibits the restoration of BEST1-dependent Cl- currents in RPE cells by gene augmentation, in contrast to the efficient rescue of loss-of-function mutations via the same approach. Moreover, we demonstrate that gain-of-function mutations are rescuable by a combination of gene augmentation with CRISPR/Cas9-mediated knockdown of endogenous BEST1 expression, providing a universal treatment strategy for all bestrophinopathy patients regardless of their mutation types.
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Affiliation(s)
- Qingqing Zhao
- Eye Center, Renmin Hospital of Wuhan University, Wuhan, China.,Department of Pharmacology and Physiology, University of Rochester, School of Medicine and Dentistry, Rochester, United States
| | - Yang Kong
- Department of Ophthalmology, Vagelos College of Physicians & Surgeons, Columbia University, New York, United States
| | - Alec Kittredge
- Department of Pharmacology, Columbia University, New York, United States
| | - Yao Li
- Department of Ophthalmology, Vagelos College of Physicians & Surgeons, Columbia University, New York, United States
| | - Yin Shen
- Eye Center, Medical Research Institute, Renmin Hospital, Wuhan University, Wuhan, China
| | - Yu Zhang
- Department of Ophthalmology, Vagelos College of Physicians & Surgeons, Columbia University, New York, United States
| | - Stephen H Tsang
- Jonas Children's Vision Care, Departments of Ophthalmology and Pathology & Cell Biology, Edward S. Harkness Eye Institute, Institute of Human Nutrition and Columbia Stem Cell Initiative, New York Presbyterian Hospital/Columbia University Irving Medical Center, New York, United States
| | - Tingting Yang
- Department of Pharmacology and Physiology, University of Rochester, School of Medicine and Dentistry, Rochester, United States.,Department of Ophthalmology, Vagelos College of Physicians & Surgeons, Columbia University, New York, United States
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13
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Miller BR, Morse AM, Borgert JE, Liu Z, Sinclair K, Gamble G, Zou F, Newman JRB, León-Novelo LG, Marroni F, McIntyre LM. Testcrosses are an efficient strategy for identifying cis-regulatory variation: Bayesian analysis of allele-specific expression (BayesASE). G3 (BETHESDA, MD.) 2021; 11:jkab096. [PMID: 33772539 PMCID: PMC8104932 DOI: 10.1093/g3journal/jkab096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/10/2021] [Indexed: 12/30/2022]
Abstract
Allelic imbalance (AI) occurs when alleles in a diploid individual are differentially expressed and indicates cis acting regulatory variation. What is the distribution of allelic effects in a natural population? Are all alleles the same? Are all alleles distinct? The approach described applies to any technology generating allele-specific sequence counts, for example for chromatin accessibility and can be applied generally including to comparisons between tissues or environments for the same genotype. Tests of allelic effect are generally performed by crossing individuals and comparing expression between alleles directly in the F1. However, a crossing scheme that compares alleles pairwise is a prohibitive cost for more than a handful of alleles as the number of crosses is at least (n2-n)/2 where n is the number of alleles. We show here that a testcross design followed by a hypothesis test of AI between testcrosses can be used to infer differences between nontester alleles, allowing n alleles to be compared with n crosses. Using a mouse data set where both testcrosses and direct comparisons have been performed, we show that the predicted differences between nontester alleles are validated at levels of over 90% when a parent-of-origin effect is present and of 60%-80% overall. Power considerations for a testcross, are similar to those in a reciprocal cross. In all applications, the testing for AI involves several complex bioinformatics steps. BayesASE is a complete bioinformatics pipeline that incorporates state-of-the-art error reduction techniques and a flexible Bayesian approach to estimating AI and formally comparing levels of AI between conditions. The modular structure of BayesASE has been packaged in Galaxy, made available in Nextflow and as a collection of scripts for the SLURM workload manager on github (https://github.com/McIntyre-Lab/BayesASE).
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Affiliation(s)
- Brecca R Miller
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
- NYU Langone Health, New York University, New York, NY 10013, USA
| | - Alison M Morse
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32608, USA
| | - Jacqueline E Borgert
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27515, USA
| | - Zihao Liu
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32608, USA
| | - Kelsey Sinclair
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32608, USA
| | - Gavin Gamble
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| | - Fei Zou
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27515, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27515, USA
| | - Jeremy R B Newman
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
- Department of Pathology, University of Florida, Gainesville, FL 32608 USA
| | - Luis G León-Novelo
- Department of Biostatistics and Data Science, University of Texas Health Science Center at Houston-University of Texas School of Public Health, Houston, TX 7703, USA
| | - Fabio Marroni
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, 33100, Italy
| | - Lauren M McIntyre
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32608, USA
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14
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Tomlinson MJ, Polson SW, Qiu J, Lake JA, Lee W, Abasht B. Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT. Sci Rep 2021; 11:3968. [PMID: 33597613 PMCID: PMC7889858 DOI: 10.1038/s41598-021-83459-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 02/01/2021] [Indexed: 12/30/2022] Open
Abstract
Differential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.
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Affiliation(s)
- M Joseph Tomlinson
- Department of Animal and Food Sciences, University of Delaware, 531 South College Ave, Newark, DE, 19716, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, USA
| | - Shawn W Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, USA.,Department of Biological Sciences, University of Delaware, Newark, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, USA
| | - Jing Qiu
- Department of Applied Economics and Statistics, University of Delaware, Newark, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, USA
| | - Juniper A Lake
- Department of Animal and Food Sciences, University of Delaware, 531 South College Ave, Newark, DE, 19716, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, USA
| | - William Lee
- Maple Leaf Farms, Inc., Leesburg, IN, 46538, USA
| | - Behnam Abasht
- Department of Animal and Food Sciences, University of Delaware, 531 South College Ave, Newark, DE, 19716, USA. .,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, USA.
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15
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Chandradoss KR, Chawla B, Dhuppar S, Nayak R, Ramachandran R, Kurukuti S, Mazumder A, Sandhu KS. CTCF-Mediated Genome Architecture Regulates the Dosage of Mitotically Stable Mono-allelic Expression of Autosomal Genes. Cell Rep 2020; 33:108302. [PMID: 33113374 DOI: 10.1016/j.celrep.2020.108302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 07/31/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
The mechanisms that guide the clonally stable random mono-allelic expression of autosomal genes remain enigmatic. We show that (1) mono-allelically expressed (MAE) genes are assorted and insulated from bi-allelically expressed (BAE) genes through CTCF-mediated chromatin loops; (2) the cell-type-specific dynamics of mono-allelic expression coincides with the gain and loss of chromatin insulator sites; (3) dosage of MAE genes is more sensitive to the loss of chromatin insulation than that of BAE genes; and (4) inactive alleles of MAE genes are significantly more insulated than active alleles and are de-repressed upon CTCF depletion. This alludes to a topology wherein the inactive alleles of MAE genes are insulated from the spatial interference of transcriptional states from the neighboring bi-allelic domains via CTCF-mediated loops. We propose that CTCF functions as a typical insulator on inactive alleles, but facilitates transcription through enhancer-linking on active allele of MAE genes, indicating widespread allele-specific regulatory roles of CTCF.
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Affiliation(s)
- Keerthivasan Raanin Chandradoss
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Bindia Chawla
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Shivnarayan Dhuppar
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Rakhee Nayak
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Rajesh Ramachandran
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Sreenivasulu Kurukuti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Kuljeet Singh Sandhu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India.
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16
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Liang ZS, Cimino I, Yalcin B, Raghupathy N, Vancollie VE, Ibarra-Soria X, Firth HV, Rimmington D, Farooqi IS, Lelliott CJ, Munger SC, O’Rahilly S, Ferguson-Smith AC, Coll AP, Logan DW. Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity. PLoS Genet 2020; 16:e1008916. [PMID: 32877400 PMCID: PMC7467316 DOI: 10.1371/journal.pgen.1008916] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/08/2020] [Indexed: 11/30/2022] Open
Abstract
Some imprinted genes exhibit parental origin specific expression bias rather than being transcribed exclusively from one copy. The physiological relevance of this remains poorly understood. In an analysis of brain-specific allele-biased expression, we identified that Trappc9, a cellular trafficking factor, was expressed predominantly (~70%) from the maternally inherited allele. Loss-of-function mutations in human TRAPPC9 cause a rare neurodevelopmental syndrome characterized by microcephaly and obesity. By studying Trappc9 null mice we discovered that homozygous mutant mice showed a reduction in brain size, exploratory activity and social memory, as well as a marked increase in body weight. A role for Trappc9 in energy balance was further supported by increased ad libitum food intake in a child with TRAPPC9 deficiency. Strikingly, heterozygous mice lacking the maternal allele (70% reduced expression) had pathology similar to homozygous mutants, whereas mice lacking the paternal allele (30% reduction) were phenotypically normal. Taken together, we conclude that Trappc9 deficient mice recapitulate key pathological features of TRAPPC9 mutations in humans and identify a role for Trappc9 and its imprinting in controlling brain development and metabolism.
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Affiliation(s)
- Zhengzheng S. Liang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Irene Cimino
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Binnaz Yalcin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, France
| | | | | | - Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Helen V. Firth
- Department of Clinical Genetics, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Debra Rimmington
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, United Kingdom
| | | | - Steven C. Munger
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Stephen O’Rahilly
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | | | - Anthony P. Coll
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Darren W. Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
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17
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Xist Repeats A and B Account for Two Distinct Phases of X Inactivation Establishment. Dev Cell 2020; 54:21-32.e5. [PMID: 32531209 DOI: 10.1016/j.devcel.2020.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 02/16/2020] [Accepted: 05/14/2020] [Indexed: 11/20/2022]
Abstract
X chromosome inactivation (XCI) is a global silencing mechanism by which XX and XY mammals equalize X-linked gene dosages. XCI begins with an establishment phase during which Xist RNA spreads and induces de novo heterochromatinization across a female X chromosome and is followed by a maintenance phase when multiple epigenetic pathways lock down the inactive X (Xi) state. Involvement of Polycomb repressive complexes 1 and 2 in XCI has been intensively studied but with conflicting conclusions regarding their recruitment and role in Xi silencing. Here, we reveal that establishment of XCI has two phases and reconcile the roles that Xist repeats A and B play in gene silencing and Polycomb recruitment. Repeat A initiates both processes, whereas repeat B bolsters or stabilizes them thereafter. Once established, XCI no longer requires repeat A during maintenance. These findings integrate disparate studies and present a unified view of Xist's role in Polycomb-mediated silencing.
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18
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Frochaux MV, Bou Sleiman M, Gardeux V, Dainese R, Hollis B, Litovchenko M, Braman VS, Andreani T, Osman D, Deplancke B. cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel. Genome Biol 2020; 21:6. [PMID: 31948474 PMCID: PMC6966807 DOI: 10.1186/s13059-019-1912-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants affect different molecular mechanisms to determine gut immunocompetence is still limited. RESULTS To address this, we perform a systems genetics analysis of the gut transcriptomes from 38 DGRP lines that were orally infected with Pseudomonas entomophila. We identify a large number of condition-specific, expression quantitative trait loci (local-eQTLs) with infection-specific ones located in regions enriched for FOX transcription factor motifs. By assessing the allelic imbalance in the transcriptomes of 19 F1 hybrid lines from a large round robin design, we independently attribute a robust cis-regulatory effect to only 10% of these detected local-eQTLs. However, additional analyses indicate that many local-eQTLs may act in trans instead. Comparison of the transcriptomes of DGRP lines that were either susceptible or resistant to Pseudomonas entomophila infection reveals nutcracker as the only differentially expressed gene. Interestingly, we find that nutcracker is linked to infection-specific eQTLs that correlate with its expression level and to enteric infection susceptibility. Further regulatory analysis reveals one particular eQTL that significantly decreases the binding affinity for the repressor Broad, driving differential allele-specific nutcracker expression. CONCLUSIONS Our collective findings point to a large number of infection-specific cis- and trans-acting eQTLs in the DGRP, including one common non-coding variant that lowers enteric infection susceptibility.
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Affiliation(s)
- Michael V. Frochaux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Current Address: Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Brian Hollis
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Current Address: Department of Biological Sciences, University of South Carolina, Columbia, South Carolina USA
| | - Maria Litovchenko
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Virginie S. Braman
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Tommaso Andreani
- Computational Biology and Data Mining Group, Institute of Molecular Biology, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Dani Osman
- Faculty of Sciences III and Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300 Lebanon
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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19
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Felts SJ, Tang X, Willett B, Van Keulen VP, Hansen MJ, Kalari KR, Pease LR. Stochastic changes in gene expression promote chaotic dysregulation of homeostasis in clonal breast tumors. Commun Biol 2019; 2:206. [PMID: 31240244 PMCID: PMC6570763 DOI: 10.1038/s42003-019-0460-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/09/2019] [Indexed: 01/21/2023] Open
Abstract
Cells within tumors vary in phenotype as a result of changes in gene expression caused by a variety of mechanisms, permitting cancers to evolve under selective pressures from immune and other homeostatic processes. Earlier, we traced apparent losses in heterozygosity (LOH) of spontaneous breast tumors from first generation (F1) intercrossed mice to atypical epigenetic modifications in the structure of DNA across the tumor genomes. Here, we describe a parallel pattern of LOH in gene expression, revealed through quantitation of parental alleles across a population of clonal tumors. We found variegated patterns of LOH, based on allelic ratio outliers in hundreds of genes, enriched in regulatory pathways typically co-opted by tumors. The frequency of outliers was correlated with transcriptional repression of a large set of homozygous genes. These findings suggest stochastic losses in gene expression across the genome of tumors generate phenotypic variation among cells, allowing clonal selection during tumor development.
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Affiliation(s)
- Sara J. Felts
- Department of Immunology, Mayo Clinic, Rochester, MN 55905 USA
| | - Xiaojia Tang
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905 USA
| | | | | | | | - Krishna R. Kalari
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905 USA
| | - Larry R. Pease
- Department of Immunology, Mayo Clinic, Rochester, MN 55905 USA
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20
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Wang Y, Gao S, Zhao Y, Chen WH, Shao JJ, Wang NN, Li M, Zhou GX, Wang L, Shen WJ, Xu JT, Deng WD, Wang W, Chen YL, Jiang Y. Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids. Zool Res 2019; 40:293-304. [PMID: 31271004 PMCID: PMC6680129 DOI: 10.24272/j.issn.2095-8137.2019.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Divergence of gene expression and alternative splicing is a crucial driving force in the evolution of species; to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expression (ASE) and allele-specific alternative splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interference of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horse×donkey (mule/hinny) and cattle×yak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, lncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptation. In conclusion, our study demonstrated that exploration of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Shan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Yue Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Wei-Huang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Jun-Jie Shao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Ni-Ni Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Guang-Xian Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Lei Wang
- Stake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining Qinghai 810016, China
| | - Wen-Jing Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Jing-Tao Xu
- Stake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining Qinghai 810016, China
| | - Wei-Dong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming Yunnan 650223, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Yu-Lin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
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21
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Ahn B, Choi MK, Yum J, Cho IC, Kim JH, Park C. Analysis of allele-specific expression using RNA-seq of the Korean native pig and Landrace reciprocal cross. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:1816-1825. [PMID: 31208168 PMCID: PMC6819674 DOI: 10.5713/ajas.19.0097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/25/2019] [Indexed: 11/27/2022]
Abstract
Objective We tried to analyze allele-specific expression in the pig neocortex using bioinformatic analysis of high-throughput sequencing results from the parental genomes and offspring transcriptomes from reciprocal crosses between Korean Native and Landrace pigs. Methods We carried out sequencing of parental genomes and offspring transcriptomes using next generation sequencing. We subsequently carried out genome scale identification of single nucleotide polymorphisms (SNPs) in two different ways using either individual genome mapping or joint genome mapping of the same breed parents that were used for the reciprocal crosses. Using parent-specific SNPs, allele-specifically expressed genes were analyzed. Results Because of the low genome coverage (~4×) of the sequencing results, most SNPs were non-informative for parental lineage determination of the expressed alleles in the offspring and were thus excluded from our analysis. Consequently, 436 SNPs covering 336 genes were applicable to measure the imbalanced expression of paternal alleles in the offspring. By calculating the read ratios of parental alleles in the offspring, we identified seven genes showing allele-biased expression (p<0.05) including three previously reported and four newly identified genes in this study. Conclusion The newly identified allele-specifically expressing genes in the neocortex of pigs should contribute to improving our knowledge on genomic imprinting in pigs. To our knowledge, this is the first study of allelic imbalance using high throughput analysis of both parental genomes and offspring transcriptomes of the reciprocal cross in outbred animals. Our study also showed the effect of the number of informative animals on the genome level investigation of allele-specific expression using RNA-seq analysis in livestock species.
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Affiliation(s)
- Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Min-Kyeung Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Joori Yum
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, Jeju 63242, Korea
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea
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22
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Matos I, Machado MP, Schartl M, Coelho MM. Allele-specific expression variation at different ploidy levels in Squalius alburnoides. Sci Rep 2019; 9:3688. [PMID: 30842567 PMCID: PMC6403402 DOI: 10.1038/s41598-019-40210-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/07/2019] [Indexed: 11/09/2022] Open
Abstract
Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides. Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides.
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Affiliation(s)
- Isa Matos
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal.,University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany
| | - Miguel P Machado
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal.,University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany.,Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Manfred Schartl
- University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany. .,Comprehensive Cancer Center, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA.
| | - Maria Manuela Coelho
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal
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23
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24
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Potter HG, Ashbrook DG, Hager R. Offspring genetic effects on maternal care. Front Neuroendocrinol 2019; 52:195-205. [PMID: 30576700 DOI: 10.1016/j.yfrne.2018.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/08/2018] [Accepted: 12/17/2018] [Indexed: 12/21/2022]
Abstract
Parental care is found widely across animal taxa and is manifest in a range of behaviours from basic provisioning in cockroaches to highly complex behaviours seen in mammals. The evolution of parental care is viewed as the outcome of an evolutionary cost/benefit trade-off between investing in current and future offspring, leading to the selection of traits in offspring that influence parental behaviour. Thus, level and quality of parental care are affected by both parental and offspring genetic differences that directly and indirectly influence parental care behaviour. While significant research effort has gone into understanding how parental genomes affect parental, and mostly maternal, behaviour, few studies have investigated how offspring genomes affect parental care. In this review, we bring together recent findings across different fields focussing on the mechanism and genetics of offspring effects on maternal care in mammals.
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Affiliation(s)
- Harry G Potter
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PT, United Kingdom.
| | - David G Ashbrook
- Department of Genetics, Genomics and Informatics, Translational Science Research Building, Room 415, University of Tennessee Health Science Center, 71 S Manassas St, Memphis, TN 38103, United States
| | - Reinmar Hager
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PT, United Kingdom
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25
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SMCHD1 Merges Chromosome Compartments and Assists Formation of Super-Structures on the Inactive X. Cell 2018; 174:406-421.e25. [PMID: 29887375 DOI: 10.1016/j.cell.2018.05.007] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 03/19/2018] [Accepted: 05/02/2018] [Indexed: 12/22/2022]
Abstract
Mammalian chromosomes are partitioned into A/B compartments and topologically associated domains (TADs). The inactive X (Xi) chromosome, however, adopts a distinct conformation without evident compartments or TADs. Here, through exploration of an architectural protein, structural-maintenance-of-chromosomes hinge domain containing 1 (SMCHD1), we probe how the Xi is reconfigured during X chromosome inactivation. A/B compartments are first fused into "S1" and "S2" compartments, coinciding with Xist spreading into gene-rich domains. SMCHD1 then binds S1/S2 compartments and merges them to create a compartment-less architecture. Contrary to current views, TADs remain on the Xi but in an attenuated state. Ablating SMCHD1 results in a persistent S1/S2 organization and strengthening of TADs. Furthermore, loss of SMCHD1 causes regional defects in Xist spreading and erosion of heterochromatic silencing. We present a stepwise model for Xi folding, where SMCHD1 attenuates a hidden layer of Xi architecture to facilitate Xist spreading.
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26
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RNA-Seq Analyses Identify Frequent Allele Specific Expression and No Evidence of Genomic Imprinting in Specific Embryonic Tissues of Chicken. Sci Rep 2017; 7:11944. [PMID: 28931927 PMCID: PMC5607270 DOI: 10.1038/s41598-017-12179-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/05/2017] [Indexed: 12/30/2022] Open
Abstract
Epigenetic and genetic cis-regulatory elements in diploid organisms may cause allele specific expression (ASE) – unequal expression of the two chromosomal gene copies. Genomic imprinting is an intriguing type of ASE in which some genes are expressed monoallelically from either the paternal allele or maternal allele as a result of epigenetic modifications. Imprinted genes have been identified in several animal species and are frequently associated with embryonic development and growth. Whether genomic imprinting exists in chickens remains debatable, as previous studies have reported conflicting evidence. Albeit no genomic imprinting has been reported in the chicken embryo as a whole, we interrogated the existence or absence of genomic imprinting in the 12-day-old chicken embryonic brain and liver by examining ASE in F1 reciprocal crosses of two highly inbred chicken lines (Fayoumi and Leghorn). We identified 5197 and 4638 ASE SNPs, corresponding to 18.3% and 17.3% of the genes with a detectable expression in the embryonic brain and liver, respectively. There was no evidence detected of genomic imprinting in 12-day-old embryonic brain and liver. While ruling out the possibility of imprinted Z-chromosome inactivation, our results indicated that Z-linked gene expression is partially compensated between sexes in chickens.
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27
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Genome-wide identification of autosomal genes with allelic imbalance of chromatin state. PLoS One 2017; 12:e0182568. [PMID: 28796844 PMCID: PMC5552117 DOI: 10.1371/journal.pone.0182568] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/20/2017] [Indexed: 11/19/2022] Open
Abstract
In mammals, monoallelic gene expression can result from X-chromosome inactivation, genomic imprinting, and random monoallelic expression (RMAE). Epigenetic regulation of RMAE is not fully understood. Here we analyze allelic imbalance in chromatin state of autosomal genes using ChIP-seq in a clonal cell line. We identify approximately 3.7% of autosomal genes that show significant differences between chromatin states of two alleles. Allelic regulation is represented among several functional gene categories including histones, chromatin modifiers, and multiple early developmental regulators. Most cases of allelic skew are produced by quantitative differences between two allelic chromatic states that belong to the same gross type (active, silent, or bivalent). Combinations of allelic states of different types are possible but less frequent. When different chromatin marks are skewed on the same gene, their skew is coordinated as a result of quantitative relationships between these marks on each individual allele. Finally, combination of allele-specific densities of chromatin marks is a quantitative predictor of allelic skew in gene expression.
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28
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Chuang TJ, Tseng YH, Chen CY, Wang YD. Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios. Sci Rep 2017; 7:7038. [PMID: 28765567 PMCID: PMC5539102 DOI: 10.1038/s41598-017-07514-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/23/2017] [Indexed: 11/23/2022] Open
Abstract
Genomic imprinting is an important epigenetic process that silences one of the parentally-inherited alleles of a gene and thereby exhibits allelic-specific expression (ASE). Detection of human imprinting events is hampered by the infeasibility of the reciprocal mating system in humans and the removal of ASE events arising from non-imprinting factors. Here, we describe a pipeline with the pattern of reciprocal allele descendants (RADs) through genotyping and transcriptome sequencing data across independent parent-offspring trios to discriminate between varied types of ASE (e.g., imprinting, genetic variation-dependent ASE, and random monoallelic expression (RME)). We show that the vast majority of ASE events are due to sequence-dependent genetic variant, which are evolutionarily conserved and may themselves play a cis-regulatory role. Particularly, 74% of non-RAD ASE events, even though they exhibit ASE biases toward the same parentally-inherited allele across different individuals, are derived from genetic variation but not imprinting. We further show that the RME effect may affect the effectiveness of the population-based method for detecting imprinting events and our pipeline can help to distinguish between these two ASE types. Taken together, this study provides a good indicator for categorization of different types of ASE, opening up this widespread and complex mechanism for comprehensive characterization.
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Affiliation(s)
| | | | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Da Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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29
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Huang WC, Ferris E, Cheng T, Hörndli CS, Gleason K, Tamminga C, Wagner JD, Boucher KM, Christian JL, Gregg C. Diverse Non-genetic, Allele-Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain. Neuron 2017; 93:1094-1109.e7. [PMID: 28238550 PMCID: PMC5774018 DOI: 10.1016/j.neuron.2017.01.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 11/27/2016] [Accepted: 01/30/2017] [Indexed: 01/19/2023]
Abstract
Interactions between genetic and epigenetic effects shape brain function, behavior, and the risk for mental illness. Random X inactivation and genomic imprinting are epigenetic allelic effects that are well known to influence genetic architecture and disease risk. Less is known about the nature, prevalence, and conservation of other potential epigenetic allelic effects in vivo in the mouse and primate brain. Here we devise genomics, in situ hybridization, and mouse genetics strategies to uncover diverse allelic effects in the brain that are not caused by imprinting or genetic variation. We found allelic effects that are developmental stage and cell type specific, that are prevalent in the neonatal brain, and that cause mosaics of monoallelic brain cells that differentially express wild-type and mutant alleles for heterozygous mutations. Finally, we show that diverse non-genetic allelic effects that impact mental illness risk genes exist in the macaque and human brain. Our findings have potential implications for mammalian brain genetics. VIDEO ABSTRACT.
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Affiliation(s)
- Wei-Chao Huang
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Elliott Ferris
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Tong Cheng
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Cornelia Stacher Hörndli
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kelly Gleason
- Department of Psychiatry, UT Southwestern, Dallas, TX 75390-9127, USA
| | - Carol Tamminga
- Department of Psychiatry, UT Southwestern, Dallas, TX 75390-9127, USA
| | - Janice D Wagner
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Kenneth M Boucher
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Cancer Biostatistics Shared Resource, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jan L Christian
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Christopher Gregg
- Robertson Neuroscience Investigator, New York Stem Cell Foundation, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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30
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Linseman T, Soubeyrand S, Martinuk A, Nikpay M, Lau P, McPherson R. Functional Validation of a Common Nonsynonymous Coding Variant in
ZC3HC1
Associated With Protection From Coronary Artery Disease. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.116.001498. [DOI: 10.1161/circgenetics.116.001498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/16/2016] [Indexed: 11/16/2022]
Abstract
Background—
Although virtually all coronary artery disease associated single-nucleotide polymorphisms identified by genome-wide association studies (GWAS) are in noncoding regions of the genome, a common polymorphism in
ZC3HC1
(rs11556924), resulting in an arginine (Arg) to histidine (His) substitution in its encoded protein, NIPA (Nuclear Interacting Partner of Anaplastic Lyphoma Kinase) is linked to a protection from coronary artery disease. NIPA plays a role in cell cycle progression, but the functional consequences of this polymorphism have not been established.
Methods and Results—
Here we demonstrate that total
ZC3HC1
expression in whole blood is similar across genotypes, despite expression being slightly biased toward the risk allele in heterozygotes. At the protein level, the protective His363 NIPA variant exhibits increased phosphorylation of a critical serine residue (Ser354) and higher protein expression as compared with the Arg363 variant. Binding experiments indicate that neither SKP1 (S-phase kinase-associated protein 1) nor CCNB1 binding were affected by the polymorphism. Despite similar nuclear distribution, NIPA His363 exhibits greater nuclear mobility. NIPA suppression results in a modest reduction of proliferation in vascular smooth muscle cells, but given low proliferative capacity, a significant effect of the variant was not noted. By contrast, we demonstrate that the protective variant reduces cell proliferation in HeLa cells.
Conclusions—
These findings extend the genetic association between rs11556924 and coronary artery disease risk by characterizing its effects on the encoded protein, NIPA. The resulting amino acid change Arg363His is associated with increased expression and nuclear mobility, as well as lower rates of cell growth in HeLa cells, further supporting a role for cell proliferation in atherosclerosis and its clinical consequences.
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Affiliation(s)
- Tara Linseman
- From the Atherogenomics Laboratory, University of Ottawa Heart Institute, Canada
| | - Sébastien Soubeyrand
- From the Atherogenomics Laboratory, University of Ottawa Heart Institute, Canada
| | - Amy Martinuk
- From the Atherogenomics Laboratory, University of Ottawa Heart Institute, Canada
| | - Majid Nikpay
- From the Atherogenomics Laboratory, University of Ottawa Heart Institute, Canada
| | - Paulina Lau
- From the Atherogenomics Laboratory, University of Ottawa Heart Institute, Canada
| | - Ruth McPherson
- From the Atherogenomics Laboratory, University of Ottawa Heart Institute, Canada
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31
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Lessing D, Dial TO, Wei C, Payer B, Carrette LLG, Kesner B, Szanto A, Jadhav A, Maloney DJ, Simeonov A, Theriault J, Hasaka T, Bedalov A, Bartolomei MS, Lee JT. A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X reactivation. Proc Natl Acad Sci U S A 2016; 113:14366-14371. [PMID: 28182563 PMCID: PMC5167172 DOI: 10.1073/pnas.1617597113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
X-chromosome inactivation is a mechanism of dosage compensation in which one of the two X chromosomes in female mammals is transcriptionally silenced. Once established, silencing of the inactive X (Xi) is robust and difficult to reverse pharmacologically. However, the Xi is a reservoir of >1,000 functional genes that could be potentially tapped to treat X-linked disease. To identify compounds that could reactivate the Xi, here we screened ∼367,000 small molecules in an automated high-content screen using an Xi-linked GFP reporter in mouse fibroblasts. Given the robust nature of silencing, we sensitized the screen by "priming" cells with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5azadC). Compounds that elicited GFP activity include VX680, MLN8237, and 5azadC, which are known to target the Aurora kinase and DNA methylation pathways. We demonstrate that the combinations of VX680 and 5azadC, as well as MLN8237 and 5azadC, synergistically up-regulate genes on the Xi. Thus, our work identifies a synergism between the DNA methylation and Aurora kinase pathways as being one of interest for possible pharmacological reactivation of the Xi.
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Affiliation(s)
- Derek Lessing
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Thomas O Dial
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Chunyao Wei
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | | | - Lieselot L G Carrette
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Barry Kesner
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Attila Szanto
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Ajit Jadhav
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - David J Maloney
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | | | | | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Jeannie T Lee
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114;
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
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32
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Weiss KM. The cat in between: Nature, nurture, . . . neither! Evol Anthropol 2016; 25:222-227. [PMID: 27753215 DOI: 10.1002/evan.21489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 12/22/2022]
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33
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Reinius B, Mold JE, Ramsköld D, Deng Q, Johnsson P, Michaëlsson J, Frisén J, Sandberg R. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. Nat Genet 2016; 48:1430-1435. [PMID: 27668657 PMCID: PMC5117254 DOI: 10.1038/ng.3678] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/29/2016] [Indexed: 12/16/2022]
Abstract
Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here we used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and freshly isolated human CD8+ T cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells' transcriptomes, with levels dependent on the cells' transcriptional activity. Notably, clonal aRME was detected, but it was surprisingly scarce (<1% of genes) and mainly affected the most weakly expressed genes. Consequently, the overwhelming majority of aRME occurs transiently within individual cells, and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells.
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Affiliation(s)
- Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Daniel Ramsköld
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Qiaolin Deng
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Per Johnsson
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
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34
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Buffering of Genetic Regulatory Networks in Drosophila melanogaster. Genetics 2016; 203:1177-90. [PMID: 27194752 DOI: 10.1534/genetics.116.188797] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/17/2016] [Indexed: 01/01/2023] Open
Abstract
Regulatory variation in gene expression can be described by cis- and trans-genetic components. Here we used RNA-seq data from a population panel of Drosophila melanogaster test crosses to compare allelic imbalance (AI) in female head tissue between mated and virgin flies, an environmental change known to affect transcription. Indeed, 3048 exons (1610 genes) are differentially expressed in this study. A Bayesian model for AI, with an intersection test, controls type I error. There are ∼200 genes with AI exclusively in mated or virgin flies, indicating an environmental component of expression regulation. On average 34% of genes within a cross and 54% of all genes show evidence for genetic regulation of transcription. Nearly all differentially regulated genes are affected in cis, with an average of 63% of expression variation explained by the cis-effects. Trans-effects explain 8% of the variance in AI on average and the interaction between cis and trans explains an average of 11% of the total variance in AI. In both environments cis- and trans-effects are compensatory in their overall effect, with a negative association between cis- and trans-effects in 85% of the exons examined. We hypothesize that the gene expression level perturbed by cis-regulatory mutations is compensated through trans-regulatory mechanisms, e.g., trans and cis by trans-factors buffering cis-mutations. In addition, when AI is detected in both environments, cis-mated, cis-virgin, and trans-mated-trans-virgin estimates are highly concordant with 99% of all exons positively correlated with a median correlation of 0.83 for cis and 0.95 for trans We conclude that the gene regulatory networks (GRNs) are robust and that trans-buffering explains robustness.
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Chamberlain AJ, Vander Jagt CJ, Hayes BJ, Khansefid M, Marett LC, Millen CA, Nguyen TTT, Goddard ME. Extensive variation between tissues in allele specific expression in an outbred mammal. BMC Genomics 2015; 16:993. [PMID: 26596891 PMCID: PMC4657355 DOI: 10.1186/s12864-015-2174-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/31/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Allele specific gene expression (ASE), with the paternal allele more expressed than the maternal allele or vice versa, appears to be a common phenomenon in humans and mice. In other species the extent of ASE is unknown, and even in humans and mice there are several outstanding questions. These include; to what extent is ASE tissue specific? how often does the direction of allele expression imbalance reverse between tissues? how often is only one of the two alleles expressed? is there a genome wide bias towards expression of the paternal or maternal allele; and finally do genes that are nearby on a chromosome share the same direction of ASE? Here we use gene expression data (RNASeq) from 18 tissues from a single cow to investigate each of these questions in turn, and then validate some of these findings in two tissues from 20 cows. RESULTS Between 40 and 100 million sequence reads were generated per tissue across three replicate samples for each of the eighteen tissues from the single cow (the discovery dataset). A bovine gene expression atlas was created (the first from RNASeq data), and differentially expressed genes in each tissue were identified. To analyse ASE, we had access to unambiguously phased genotypes for all heterozygous variants in the cow's whole genome sequence, where these variants were homozygous in the whole genome sequence of her sire, and as a result we were able to map reads to parental genomes, to determine SNP and genes showing ASE in each tissue. In total 25,251 heterozygous SNP within 7985 genes were tested for ASE in at least one tissue. ASE was pervasive, 89 % of genes tested had significant ASE in at least one tissue. This large proportion of genes displaying ASE was confirmed in the two tissues in a validation dataset. For individual tissues the proportion of genes showing significant ASE varied from as low as 8-16 % of those tested in thymus to as high as 71-82 % of those tested in lung. There were a number of cases where the direction of allele expression imbalance reversed between tissues. For example the gene SPTY2D1 showed almost complete paternal allele expression in kidney and thymus, and almost complete maternal allele expression in the brain caudal lobe and brain cerebellum. Mono allelic expression (MAE) was common, with 1349 of 4856 genes (28 %) tested with more than one heterozygous SNP showing MAE. Across all tissues, 54.17 % of all genes with ASE favoured the paternal allele. Genes that are closely linked on the chromosome were more likely to show higher expression of the same allele (paternal or maternal) than expected by chance. We identified several long runs of neighbouring genes that showed either paternal or maternal ASE, one example was five adjacent genes (GIMAP8, GIMAP7 copy1, GIMAP4, GIMAP7 copy 2 and GIMAP5) that showed almost exclusive paternal expression in brain caudal lobe. CONCLUSIONS Investigating the extent of ASE across 18 bovine tissues in one cow and two tissues in 20 cows demonstrated 1) ASE is pervasive in cattle, 2) the ASE is often MAE but ranges from MAE to slight overexpression of the major allele, 3) the ASE is most often tissue specific and that more than half the time displays divergent allele specific expression patterns across tissues, 4) across all genes there is a slight bias towards expression of the paternal allele and 5) genes expressing the same parental allele are clustered together more than expected by chance, and there are several runs of large numbers of genes expressing the same parental allele.
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Affiliation(s)
- Amanda J Chamberlain
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
| | - Christy J Vander Jagt
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
| | - Benjamin J Hayes
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- La Trobe University, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
| | - Majid Khansefid
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Institute of Land and Food, University of Melbourne, Royal Parade, Parkville, Australia.
| | - Leah C Marett
- Department of Economic Development, Jobs, Transport and Resources, 1301 Hazeldean Rd, Ellinbank, Australia.
| | - Catriona A Millen
- Dairy Futures Cooperative Research Centre, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Institute of Land and Food, University of Melbourne, Royal Parade, Parkville, Australia.
| | - Thuy T T Nguyen
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
| | - Michael E Goddard
- Department of Economic Development, Jobs, Transport and Resources, Agribiosciences Building, 5 Ring Rd, Bundoora, Australia.
- Institute of Land and Food, University of Melbourne, Royal Parade, Parkville, Australia.
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