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Rückert T, Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev 2024; 323:80-106. [PMID: 38506411 DOI: 10.1111/imr.13324] [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: 03/21/2024]
Abstract
Clonal expansion of antigen-specific lymphocytes is the fundamental mechanism enabling potent adaptive immune responses and the generation of immune memory. Accompanied by pronounced epigenetic remodeling, the massive proliferation of individual cells generates a critical mass of effectors for the control of acute infections, as well as a pool of memory cells protecting against future pathogen encounters. Classically associated with the adaptive immune system, recent work has demonstrated that innate immune memory to human cytomegalovirus (CMV) infection is stably maintained as large clonal expansions of natural killer (NK) cells, raising questions on the mechanisms for clonal selection and expansion in the absence of re-arranged antigen receptors. Here, we discuss clonal NK cell memory in the context of the mechanisms underlying clonal competition of adaptive lymphocytes and propose alternative selection mechanisms that might decide on the clonal success of their innate counterparts. We propose that the integration of external cues with cell-intrinsic sources of heterogeneity, such as variegated receptor expression, transcriptional states, and somatic variants, compose a bottleneck for clonal selection, contributing to the large size of memory NK cell clones.
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Affiliation(s)
- Timo Rückert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Chiara Romagnani
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
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2
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Mendelevich A, Gupta S, Pakharev A, Teodosiadis A, Mironov AA, Gimelbrant AA. Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. Bioinformatics 2023; 39:i431-i439. [PMID: 37387154 DOI: 10.1093/bioinformatics/btad254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach which is highly accurate at only a small fraction of the cost. RESULTS We show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, and Caenorhabditis elegans. Our new approach, controlFreq, enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of ∼5%. AVAILABILITY AND IMPLEMENTATION Analysis pipeline for this approach is available at GitHub as R package controlFreq (github.com/gimelbrantlab/controlFreq).
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Affiliation(s)
- Asia Mendelevich
- Altius Institute for Biomedical Sciences, 2211 Elliott Ave, Seattle, WA 98121, United States
| | - Saumya Gupta
- Stem Cell Program, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138, United States
| | | | - Athanasios Teodosiadis
- Altius Institute for Biomedical Sciences, 2211 Elliott Ave, Seattle, WA 98121, United States
| | - Andrey A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 1-73 Vorobiovy Gory, Lab. Bldg B, Moscow 119992, Russia
- Institute of Information Transmission Problems, Russian Academy of Sciences, 19 Bolshoi Karetny per., Moscow 127994, Russia
| | - Alexander A Gimelbrant
- Altius Institute for Biomedical Sciences, 2211 Elliott Ave, Seattle, WA 98121, United States
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Mendelevich A, Gupta S, Pakharev A, Teodosiadis A, Mironov AA, Gimelbrant AA. Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.11.528027. [PMID: 36798258 PMCID: PMC9934692 DOI: 10.1101/2023.02.11.528027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Motivation Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach that is highly accurate at only a small fraction of the cost. Results We show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, and C.elegans . Our new approach, controlFreq , enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of ~ 5%. Availability Analysis pipeline for this approach is available at GitHub as R package controlFreq ( github.com/gimelbrantlab/controlFreq ). Contact agimelbrant@altius.org.
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Affiliation(s)
| | - Saumya Gupta
- Stem Cell Program, Boston Children’s Hospital, Boston, MA, USA,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | | | - Andrey A. Mironov
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia,Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A. Gimelbrant
- Altius Institute for Biomedical Sciences, Seattle, WA, USA,To whom correspondence should be addressed. Contact:
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4
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Balasooriya GI, Spector DL. Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage. Nat Commun 2022; 13:5984. [PMID: 36216821 PMCID: PMC9550772 DOI: 10.1038/s41467-022-33722-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/27/2022] [Indexed: 11/29/2022] Open
Abstract
Each mammalian autosomal gene is represented by two alleles in diploid cells. To our knowledge, no insights have been made in regard to allele-specific regulatory mechanisms of autosomes. Here we use allele-specific single cell transcriptomic analysis to elucidate the establishment of monoallelic gene expression in the cardiac lineage. We find that monoallelically expressed autosomal genes in mESCs and mouse blastocyst cells are differentially regulated based on the genetic background of the parental alleles. However, the genetic background of the allele does not affect the establishment of monoallelic genes in differentiated cardiomyocytes. Additionally, we observe epigenetic differences between deterministic and random autosomal monoallelic genes. Moreover, we also find a greater contribution of the maternal versus paternal allele to the development and homeostasis of cardiac tissue and in cardiac health, highlighting the importance of maternal influence in male cardiac tissue homeostasis. Our findings emphasize the significance of allele-specific insights into gene regulation in development, homeostasis and disease.
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Kubasova N, Alves-Pereira CF, Gupta S, Vinogradova S, Gimelbrant A, Barreto VM. In Vivo Clonal Analysis Reveals Random Monoallelic Expression in Lymphocytes That Traces Back to Hematopoietic Stem Cells. Front Cell Dev Biol 2022; 10:827774. [PMID: 36003148 PMCID: PMC9393635 DOI: 10.3389/fcell.2022.827774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Evaluating the epigenetic landscape in the stem cell compartment at the single-cell level is essential to assess the cells’ heterogeneity and predict their fate. Here, using a genome-wide transcriptomics approach in vivo, we evaluated the allelic expression imbalance in the progeny of single hematopoietic cells (HSCs) as a read-out of epigenetic marking. After 4 months of extensive proliferation and differentiation, we found that X-chromosome inactivation (XCI) is tightly maintained in all single-HSC derived hematopoietic cells. In contrast, the vast majority of the autosomal genes did not show clonal patterns of random monoallelic expression (RME). However, a persistent allele-specific autosomal transcription in HSCs and their progeny was found in a rare number of cases, none of which has been previously reported. These data show that: 1) XCI and RME in the autosomal chromosomes are driven by different mechanisms; 2) the previously reported high frequency of genes under RME in clones expanded in vitro (up to 15%) is not found in clones undergoing multiple differentiation steps in vivo; 3) prior to differentiation, HSCs have stable patterns of autosomal RME. We propose that most RME patterns in autosomal chromosomes are erased and established de novo during cell lineage differentiation.
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Affiliation(s)
- Nadiya Kubasova
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- Genetagus, Egas Moniz – Cooperativa de Ensino Superior, CRL, Monte de Caparica, Portugal
| | - Clara F. Alves-Pereira
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Saumya Gupta
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Svetlana Vinogradova
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Alexander Gimelbrant
- Center of Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
| | - Vasco M. Barreto
- Chronic Diseases Research Centre, Nova Medical School, CEDOC, Lisbon, Portugal
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Costa da Caparica, Portugal
- *Correspondence: Vasco M. Barreto, ; Alexander Gimelbrant,
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Gupta S, Lafontaine DL, Vigneau S, Mendelevich A, Vinogradova S, Igarashi KJ, Bortvin A, Alves-Pereira CF, Nag A, Gimelbrant AA. RNA sequencing-based screen for reactivation of silenced alleles of autosomal genes. G3 (BETHESDA, MD.) 2022; 12:6472352. [PMID: 35100361 PMCID: PMC9210281 DOI: 10.1093/g3journal/jkab428] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 12/05/2021] [Indexed: 12/12/2022]
Abstract
In mammalian cells, maternal and paternal alleles usually have similar transcriptional activity. Epigenetic mechanisms such as X-chromosome inactivation (XCI) and imprinting were historically viewed as rare exceptions to this rule. Discovery of autosomal monoallelic autosomal expression (MAE) a decade ago revealed an additional allele-specific mode regulating thousands of mammalian genes. Despite MAE prevalence, its mechanistic basis remains unknown. Using an RNA sequencing-based screen for reactivation of silenced alleles, we identified DNA methylation as key mechanism of MAE mitotic maintenance. In contrast with the all-or-nothing allelic choice in XCI, allele-specific expression in MAE loci is tunable, with exact allelic imbalance dependent on the extent of DNA methylation. In a subset of MAE genes, allelic imbalance was insensitive to DNA demethylation, implicating additional mechanisms in MAE maintenance in these loci. Our findings identify a key mechanism of MAE maintenance and provide basis for understanding the biological role of MAE.
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Affiliation(s)
| | | | - Sebastien Vigneau
- Department of Cancer Biology and Center of Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Asia Mendelevich
- Department of Cancer Biology and Center of Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Svetlana Vinogradova
- Department of Cancer Biology and Center of Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
| | - Kyomi J Igarashi
- Department of Cancer Biology and Center of Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
| | - Andrew Bortvin
- Department of Cancer Biology and Center of Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
| | - Clara F Alves-Pereira
- Department of Cancer Biology and Center of Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anwesha Nag
- Department of Cancer Biology and Center of Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
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Lim KS, Kim HC, Choi BH, Son JW, Lee KT, Choi TJ, Cho YM, Chai HH, Park JE, Park W, Lim C, Kim JM, Lim D. Identification of Monoallelically Expressed Genes Associated with Economic Traits in Hanwoo (Korean Native Cattle). Animals (Basel) 2021; 12:ani12010084. [PMID: 35011190 PMCID: PMC8749587 DOI: 10.3390/ani12010084] [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: 10/08/2021] [Revised: 12/25/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Hanwoo, an indigenous Korean cattle breed, has been genetically improved by selecting superior sires called Korean-proven bulls. However, cows still contribute half of the genetic stock of their offspring, and allelic-specific expressed genes have potential, as selective targets of cows, to enhance genetic gain. The aim of this study is to identify genes that have MAEs based on both the genome and transcriptome and to estimate their effects on breeding values (BVs) for economically important traits in Hanwoo. We generated resequencing data for the parents and RNA-sequencing data for the muscle, fat, and brain tissues of the offspring. A total of 3801 heterozygous single nucleotide polymorphisms (SNPs) in offspring were identified and they were located in 1569 genes. Only 14 genes showed MAE (seven expressing maternal alleles and seven expressing paternal alleles). Tissue-specific MAE was observed, and LANCL1 showed maternal allele expression across all tissues. MAE genes were enriched for the biological process of cell death and angiogenesis, which included ACKR3 and PDCL3 genes, whose SNPs were significantly associated with BVs of lean meat production-related traits, such as weight at 12 months of age, carcass weight, and loin eye area. In the current study, monoallelically expressed genes were identified in various adult tissues and these genes were associated with genetic capacity in Hanwoo.
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Affiliation(s)
- Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Hyung-Chul Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Ju-Whan Son
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Tae-Jeong Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Yong-Min Cho
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
| | - Chiwoong Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Gyeonggi-do, Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Jeollabuk-do, Korea
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8
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Basilicata MF, Keller Valsecchi CI. The good, the bad, and the ugly: Evolutionary and pathological aspects of gene dosage alterations. PLoS Genet 2021; 17:e1009906. [PMID: 34882671 PMCID: PMC8659298 DOI: 10.1371/journal.pgen.1009906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Diploid organisms contain a maternal and a paternal genome complement that is thought to provide robustness and allow developmental progression despite genetic perturbations that occur in heterozygosity. However, changes affecting gene dosage from the chromosome down to the individual gene level possess a significant pathological potential and can lead to developmental disorders (DDs). This indicates that expression from a balanced gene complement is highly relevant for proper cellular and organismal function in eukaryotes. Paradoxically, gene and whole chromosome duplications are a principal driver of evolution, while heteromorphic sex chromosomes (XY and ZW) are naturally occurring aneuploidies important for sex determination. Here, we provide an overview of the biology of gene dosage at the crossroads between evolutionary benefit and pathogenicity during disease. We describe the buffering mechanisms and cellular responses to alterations, which could provide a common ground for the understanding of DDs caused by copy number alterations.
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9
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Sands B, Yun S, Mendenhall AR. Introns control stochastic allele expression bias. Nat Commun 2021; 12:6527. [PMID: 34764277 PMCID: PMC8585970 DOI: 10.1038/s41467-021-26798-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Monoallelic expression (MAE) or extreme allele bias can account for incomplete penetrance, missing heritability and non-Mendelian diseases. In cancer, MAE is associated with shorter patient survival times and higher tumor grade. Prior studies showed that stochastic MAE is caused by stochastic epigenetic silencing, in a gene and tissue-specific manner. Here, we used C. elegans to study stochastic MAE in vivo. We found allele bias/MAE to be widespread within C. elegans tissues, presenting as a continuum from fully biallelic to MAE. We discovered that the presence of introns within alleles robustly decreases MAE. We determined that introns control MAE at distinct loci, in distinct cell types, with distinct promoters, and within distinct coding sequences, using a 5'-intron position-dependent mechanism. Bioinformatic analysis showed human intronless genes are significantly enriched for MAE. Our experimental evidence demonstrates a role for introns in regulating MAE, possibly explaining why some mutations within introns result in disease.
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Affiliation(s)
- Bryan Sands
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Soo Yun
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Alexander R. Mendenhall
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
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10
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Fu R, Qin P, Zou X, Hu Z, Hong N, Wang Y, Jin W. A Comprehensive Characterization of Monoallelic Expression During Hematopoiesis and Leukemogenesis via Single-Cell RNA-Sequencing. Front Cell Dev Biol 2021; 9:702897. [PMID: 34722498 PMCID: PMC8548578 DOI: 10.3389/fcell.2021.702897] [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: 04/30/2021] [Accepted: 09/13/2021] [Indexed: 12/30/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is becoming a powerful tool to investigate monoallelic expression (MAE) in various developmental and pathological processes. However, our knowledge of MAE during hematopoiesis and leukemogenesis is limited. In this study, we conducted a systematic interrogation of MAEs in bone marrow mononuclear cells (BMMCs) at single-cell resolution to construct a MAE atlas of BMMCs. We identified 1,020 constitutive MAEs in BMMCs, which included imprinted genes such as MEG8, NAP1L5, and IRAIN. We classified the BMMCs into six cell types and identified 74 cell type specific MAEs including MTSS1, MOB1A, and TCF12. We further identified 114 random MAEs (rMAEs) at single-cell level, with 78.1% single-allele rMAE and 21.9% biallelic mosaic rMAE. Many MAEs identified in BMMCs have not been reported and are potentially hematopoietic specific, supporting MAEs are functional relevance. Comparison of BMMC samples from a leukemia patient with multiple clinical stages showed the fractions of constitutive MAE were correlated with fractions of leukemia cells in BMMCs. Further separation of the BMMCs into leukemia cells and normal cells showed that leukemia cells have much higher constitutive MAE and rMAEs than normal cells. We identified the leukemia cell-specific MAEs and relapsed leukemia cell-specific MAEs, which were enriched in immune-related functions. These results indicate MAE is prevalent and is an important gene regulation mechanism during hematopoiesis and leukemogenesis. As the first systematical interrogation of constitutive MAEs, cell type specific MAEs, and rMAEs during hematopoiesis and leukemogenesis, the study significantly increased our knowledge about the features and functions of MAEs.
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Affiliation(s)
- Ruiqing Fu
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Pengfei Qin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xianghui Zou
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yun Wang
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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11
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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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12
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Semicoordinated allelic-bursting shape dynamic random monoallelic expression in pregastrulation embryos. iScience 2021; 24:102954. [PMID: 34458702 PMCID: PMC8379509 DOI: 10.1016/j.isci.2021.102954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 01/14/2023] Open
Abstract
Recently, allele-specific single-cell RNA-seq analysis has demonstrated widespread dynamic random monoallelic expression of autosomal genes (aRME) in different cell types. However, the prevalence of dynamic aRME during pregastrulation remains unknown. Here, we show that dynamic aRME is widespread in different lineages of pregastrulation embryos. Additionally, the origin of dynamic aRME remains elusive. It is believed that independent transcriptional bursting from each allele leads to dynamic aRME. Here, we show that allelic burst is not perfectly independent; instead it happens in a semicoordinated fashion. Importantly, we show that semicoordinated allelic bursting of genes, particularly with low burst frequency, leads to frequent asynchronous allelic bursting, thereby contributing to dynamic aRME. Furthermore, we found that coordination of allelic bursting is lineage specific and genes regulating the development have a higher degree of coordination. Altogether, our study provides significant insights into the prevalence and origin of dynamic aRME and their developmental relevance during early development. Dynamic aRME is widespread in different lineages of pregastrulation embryos Semicoordinated bursting of genes with low burst frequency leads to dynamic aRME Degree of coordination of allelic bursting is lineage specific Developmental genes have higher degree of coordination of allelic bursting
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13
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Marion-Poll L, Forêt B, Zielinski D, Massip F, Attia M, Carter AC, Syx L, Chang HY, Gendrel AV, Heard E. Locus specific epigenetic modalities of random allelic expression imbalance. Nat Commun 2021; 12:5330. [PMID: 34504093 PMCID: PMC8429725 DOI: 10.1038/s41467-021-25630-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/19/2021] [Indexed: 01/02/2023] Open
Abstract
Most autosomal genes are thought to be expressed from both alleles, with some notable exceptions, including imprinted genes and genes showing random monoallelic expression (RME). The extent and nature of RME has been the subject of debate. Here we investigate the expression of several candidate RME genes in F1 hybrid mouse cells before and after differentiation, to define how they become persistently, monoallelically expressed. Clonal monoallelic expression is not present in embryonic stem cells, but we observe high frequencies of monoallelism in neuronal progenitor cells by assessing expression status in more than 200 clones. We uncover unforeseen modes of allelic expression that appear to be gene-specific and epigenetically regulated. This non-canonical allelic regulation has important implications for development and disease, including autosomal dominant disorders and opens up therapeutic perspectives.
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Affiliation(s)
- Lucile Marion-Poll
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France.
- Directors' research, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | - Benjamin Forêt
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Dina Zielinski
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
- Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, Paris, France
| | - Florian Massip
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mikael Attia
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Laurène Syx
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
- Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, Paris, France
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Anne-Valerie Gendrel
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France.
| | - Edith Heard
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France.
- Directors' research, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Collège de France, Paris, France.
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14
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Mendelevich A, Vinogradova S, Gupta S, Mironov AA, Sunyaev SR, Gimelbrant AA. Replicate sequencing libraries are important for quantification of allelic imbalance. Nat Commun 2021; 12:3370. [PMID: 34099647 PMCID: PMC8184992 DOI: 10.1038/s41467-021-23544-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/30/2021] [Indexed: 12/13/2022] Open
Abstract
A sensitive approach to quantitative analysis of transcriptional regulation in diploid organisms is analysis of allelic imbalance (AI) in RNA sequencing (RNA-seq) data. A near-universal practice in such studies is to prepare and sequence only one library per RNA sample. We present theoretical and experimental evidence that data from a single RNA-seq library is insufficient for reliable quantification of the contribution of technical noise to the observed AI signal; consequently, reliance on one-replicate experimental design can lead to unaccounted-for variation in error rates in allele-specific analysis. We develop a computational approach, Qllelic, that accurately accounts for technical noise by making use of replicate RNA-seq libraries. Testing on new and existing datasets shows that application of Qllelic greatly decreases false positive rate in allele-specific analysis while conserving appropriate signal, and thus greatly improves reproducibility of AI estimates. We explore sources of technical overdispersion in observed AI signal and conclude by discussing design of RNA-seq studies addressing two biologically important questions: quantification of transcriptome-wide AI in one sample, and differential analysis of allele-specific expression between samples.
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Affiliation(s)
- Asia Mendelevich
- Skolkovo Institute of Science and Technology, Moscow, Russia.
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA.
| | - Svetlana Vinogradova
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Saumya Gupta
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Andrey A Mironov
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, USA
| | - Alexander A Gimelbrant
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA.
- Broad Institute of Harvard and MIT, Cambridge, USA.
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15
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Dini P, Kalbfleisch T, Uribe-Salazar JM, Carossino M, Ali HES, Loux SC, Esteller-Vico A, Norris JK, Anand L, Scoggin KE, Rodriguez Lopez CM, Breen J, Bailey E, Daels P, Ball BA. Parental bias in expression and interaction of genes in the equine placenta. Proc Natl Acad Sci U S A 2021; 118:e2006474118. [PMID: 33853939 PMCID: PMC8072238 DOI: 10.1073/pnas.2006474118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a workflow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.
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Affiliation(s)
- Pouya Dini
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Theodore Kalbfleisch
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202
| | - José M Uribe-Salazar
- Department of Biochemistry and Molecular Medicine, Genome Center, Medical Investigation of Neurodevelopmental Disorders Institute, University of California, Davis, CA 95616
| | - Mariano Carossino
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Theriogenology Department, Faculty of Veterinary Medicine, University of Mansoura, 35516, Egypt
| | - Shavahn C Loux
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Alejandro Esteller-Vico
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Jamie K Norris
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Carlos M Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Ernest Bailey
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Peter Daels
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Barry A Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503;
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16
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Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum. Sci Rep 2021; 11:2954. [PMID: 33536552 PMCID: PMC7859220 DOI: 10.1038/s41598-021-82529-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/15/2021] [Indexed: 01/04/2023] Open
Abstract
Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.
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17
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Rv P, Sundaresh A, Karunyaa M, Arun A, Gayen S. Autosomal Clonal Monoallelic Expression: Natural or Artifactual? Trends Genet 2020; 37:206-211. [PMID: 33234351 DOI: 10.1016/j.tig.2020.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 01/08/2023]
Abstract
The prevalence of mitotically heritable clonal random monoallelic expression of autosomal genes (aRME) remains controversial. Specifically, presence of clonal aRME is well supported in vitro but remains elusive in vivo. Here, we provide critical insights into this matter and discuss whether prevalent clonal aRME is natural or artifactual.
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Affiliation(s)
- P Rv
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India
| | - A Sundaresh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India
| | - M Karunyaa
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India
| | - A Arun
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India
| | - S Gayen
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore-560012, India.
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18
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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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19
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Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells. Nat Genet 2020; 52:709-718. [PMID: 32601473 PMCID: PMC7610382 DOI: 10.1038/s41588-020-0645-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/12/2020] [Indexed: 12/28/2022]
Abstract
Propagation of clonal regulatory programs contributes to cancer development. It is poorly understood how epigenetic mechanisms interact with genetic drivers to shape this process. Here, we combine single-cell analysis of transcription and DNA methylation with a Luria-Delbrück experimental design to demonstrate the existence of clonally stable epigenetic memory in multiple types of cancer cells. Longitudinal transcriptional and genetic analysis of clonal colon cancer cell populations reveals a slowly drifting spectrum of epithelial-to-mesenchymal transcriptional identities that is seemingly independent of genetic variation. DNA methylation landscapes correlate with these identities but also reflect an independent clock-like methylation loss process. Methylation variation can be explained as an effect of global trans-acting factors in most cases. However, for a specific class of promoters-in particular, cancer-testis antigens-de-repression is correlated with and probably driven by loss of methylation in cis. This study indicates how genetic sub-clonal structure in cancer cells can be diversified by epigenetic memory.
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20
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Li Y, Li T, Tang Y, Zhan Z, Ding L, Song L, Yu T, Yang Y, Ma J, Zhang Y, Zhou Y, Gu S, Xu M, Gao Y, Li Y. The function of a heterozygous p53 mutation in a Li-Fraumeni syndrome patient. PLoS One 2020; 15:e0234262. [PMID: 32516327 PMCID: PMC7282642 DOI: 10.1371/journal.pone.0234262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/21/2020] [Indexed: 11/29/2022] Open
Abstract
p53 is one of the most extensively studied proteins in cancer research. Mutations in p53 generally abolish normal p53 function, and some mutants can gain new oncogenic functions. However, the mechanisms underlying p53 mutation-driven cancer remains to be elucidated. Our study investigated the function of a heterozygous p53 mutation (p.Asn268Glufs*4) in a Li-Fraumeni syndrome (LFS) patient. We used episomal technology to perform somatic reprogramming, and used molecular and cell biology methods to determine the p53 mutation levels in patient-originated induced pluripotent stem (iPS) cells at the RNA and protein levels. We found that p53 protein expression was not increased in this patient’s somatic cells compared with those of a healthy control. p53 mutation facilitates the proliferation of tumor cells by inhibiting apoptosis and promoting cell division. It can inhibit the efficiency of somatic reprogramming by inhibiting OCT4 expression during reprogramming stage. Moreover, not all p53 mutant iPS cell lines have mutant p53 RNA sequences. A small percentage of mutant p53 mRNA is present in the somatic cells from the patient and his mother. In summary, this p53 mutation can promote tumor cell proliferation, inhibit somatic reprogramming, and exhibit random p53 allelic expression of heterozygous mutations in the patient and iPS cells which may be one of the reasons why the people with p53 mutations develop cancer at random. This finding suggested that mutant p53 allelic expression should be added to the risk forecasting of cancer.
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Affiliation(s)
- Yang Li
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Li
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuejia Tang
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyan Zhan
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lixia Ding
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lili Song
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingting Yu
- Molecular Biological Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Yang
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Ma
- Department of Pathology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingwen Zhang
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Zhou
- Department of Radiology, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Song Gu
- Department of General Surgery/Surgical Oncology Center, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Xu
- Department of General Surgery/Surgical Oncology Center, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (YL); (YG); (MX)
| | - Yijin Gao
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (YL); (YG); (MX)
| | - Yanxin Li
- Department of Hematology & Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (YL); (YG); (MX)
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21
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Kim J, Frey WD, Sharma K, Ghimire S, Teruyama R, Stubbs L. Allele-specific enhancer interaction at the Peg3 imprinted domain. PLoS One 2019; 14:e0224287. [PMID: 31639176 PMCID: PMC6804975 DOI: 10.1371/journal.pone.0224287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The parental allele specificity of mammalian imprinted genes has been evolutionarily well conserved, although its functional constraints and associated mechanisms are not fully understood. In the current study, we generated a mouse mutant with switched active alleles driving the switch from paternal-to-maternal expression for Peg3 and the maternal-to-paternal expression for Zim1. The expression levels of Peg3 and Zim1, but not the spatial expression patterns, within the brain showed clear differences between wild type and mutant animals. We identified putative enhancers localized upstream of Peg3 that displayed allele-biased DNA methylation, and that also participate in allele-biased chromosomal conformations with regional promoters. Most importantly, these data suggest for the first time that long-distance enhancers may contribute to allelic expression within imprinted domains through allele-biased interactions with regional promoters.
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Affiliation(s)
- Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
| | - Wesley D. Frey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Kaustubh Sharma
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Subash Ghimire
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Ryoichi Teruyama
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Lisa Stubbs
- Cell and Developmental Biology, Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
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22
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Göppner C, Orozco IJ, Hoegg-Beiler MB, Soria AH, Hübner CA, Fernandes-Rosa FL, Boulkroun S, Zennaro MC, Jentsch TJ. Pathogenesis of hypertension in a mouse model for human CLCN2 related hyperaldosteronism. Nat Commun 2019; 10:4678. [PMID: 31615979 PMCID: PMC6794291 DOI: 10.1038/s41467-019-12113-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 08/21/2019] [Indexed: 12/31/2022] Open
Abstract
Human primary aldosteronism (PA) can be caused by mutations in several ion channel genes but mouse models replicating this condition are lacking. We now show that almost all known PA-associated CLCN2 mutations markedly increase ClC-2 chloride currents and generate knock-in mice expressing a constitutively open ClC-2 Cl− channel as mouse model for PA. The Clcn2op allele strongly increases the chloride conductance of zona glomerulosa cells, provoking a strong depolarization and increasing cytoplasmic Ca2+ concentration. Clcn2op mice display typical features of human PA, including high serum aldosterone in the presence of low renin activity, marked hypertension and hypokalemia. These symptoms are more pronounced in homozygous Clcn2op/op than in heterozygous Clcn2+/op mice. This difference is attributed to the unexpected finding that only ~50 % of Clcn2+/op zona glomerulosa cells are depolarized. By reproducing essential features of human PA, Clcn2op mice are a valuable model to study the pathological mechanisms underlying this disease. Mutations in the chloride channel ClC-2 have been found in primary aldosteronism (PA). Here, Göppner et al. generate transgenic mice expressing a mutant form of ClC-2 that displays increased chloride currents like patient mutations, and find it recapitulates the key pathological features of PA.
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Affiliation(s)
- Corinna Göppner
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Ian J Orozco
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Maja B Hoegg-Beiler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Audrey H Soria
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | | | - Fabio L Fernandes-Rosa
- INSERM, UMRS_970, Paris Cardiovascular Research Center, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Sheerazed Boulkroun
- INSERM, UMRS_970, Paris Cardiovascular Research Center, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Maria-Christina Zennaro
- INSERM, UMRS_970, Paris Cardiovascular Research Center, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Génétique, Paris, France
| | - Thomas J Jentsch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany. .,Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany. .,NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany.
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23
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Lim KS, Chang SS, Choi BH, Lee SH, Lee KT, Chai HH, Park JE, Park W, Lim D. Genome-Wide Analysis of Allele-Specific Expression Patterns in Seventeen Tissues of Korean Cattle (Hanwoo). Animals (Basel) 2019; 9:ani9100727. [PMID: 31561539 PMCID: PMC6826869 DOI: 10.3390/ani9100727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022] Open
Abstract
The functional hemizygosity could be caused by the MAE of a given gene and it can be one of the sources to affect the phenotypic variation in cattle. We aimed to identify MAE genes across the transcriptome in Korean cattle (Hanwoo). For three Hanwoo family trios, the transcriptome data of 17 tissues were generated in three offspring. Sixty-two MAE genes had a monoallelic expression in at least one tissue. Comparing genotypes among each family trio, the preferred alleles of 18 genes were identified (maternal expression, n = 9; paternal expression, n = 9). The MAE genes are involved in gene regulation, metabolic processes, and immune responses, and in particular, six genes encode transcription factors (FOXD2, FOXM1, HTATSF1, SCRT1, NKX6-2, and UBN1) with tissue-specific expression. In this study, we report genome-wide MAE genes in seventeen tissues of adult cattle. These results could help to elucidate epigenetic effects on phenotypic variation in Hanwoo.
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Affiliation(s)
- Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
| | - Sun-Sik Chang
- Hanwoo Research Institute, National Institute of Animal Science, Rural Development Administration, Pyeongchang 25340, Korea.
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea.
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
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24
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Kondo S, Kato H, Suzuki Y, Takada T, Eitoku M, Shiroishi T, Suganuma N, Sugano S, Kiyosawa H. Monoallelic, antisense and total RNA transcription in an in vitro neural differentiation system based on F1 hybrid mice. J Cell Sci 2019; 132:jcs.228973. [PMID: 31409693 DOI: 10.1242/jcs.228973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/04/2019] [Indexed: 11/20/2022] Open
Abstract
We developed an in vitro system to differentiate embryonic stem cells (ESCs) derived from reciprocally crossed F1 hybrid mice into neurons, and used it to investigate poly(A)+ and total RNA transcription at different stages of cell differentiation. By comparing expression profiles of transcripts assembled from 20 RNA sequencing datasets [2 alleles×(2 cell lines×4 time-points+2 mouse brains)], the relative influence of strain, cell and parent specificities to overall expression could be assessed. Divergent expression profiles of ESCs converged tightly at neural progenitor stage. Patterns of temporal variation of monoallelically expressed transcripts and antisense transcripts were quantified. Comparison of sense and antisense transcript pairs within the poly(A)+ sample, within the total RNA sample, and across poly(A)+ and total RNA samples revealed distinct rates of pairs showing anti-correlated expression variation. Unique patterns of sharing of poly(A)+ and poly(A)- transcription were identified in distinct RNA species. Regulation and functionality of monoallelic expression, antisense transcripts and poly(A)- transcription remain elusive. We demonstrated the effectiveness of our approach to capture these transcriptional activities, and provided new resources to elucidate the mammalian developmental transcriptome.
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Affiliation(s)
- Shinji Kondo
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan
| | - Hidemasa Kato
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Toyoyuki Takada
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan.,Mammalian Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Masamitsu Eitoku
- Department of Environmental Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Toshihiko Shiroishi
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan.,Mammalian Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Narufumi Suganuma
- Department of Environmental Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hidenori Kiyosawa
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan .,Department of Environmental Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
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25
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Mio C, Grani G, Durante C, Damante G. Molecular defects in thyroid dysgenesis. Clin Genet 2019; 97:222-231. [PMID: 31432505 DOI: 10.1111/cge.13627] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/17/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022]
Abstract
Congenital hypothyroidism (CH) is a neonatal endocrine disorder that might occur as itself or be associated to congenital extra-thyroidal defects. About 85% of affected subjects experience thyroid dysgenesis (TD), characterized by defect in thyroid gland development. In vivo experiments on null mice paved the way for the identification of genes involved thyroid morphogenesis and development, whose mutation has been strongly associated to TD. Most of them are thyroid-specific transcription factors expressed during early thyroid development. Despite the arduous effort in unraveling the genetics of TD in animal models, up to now these data have been discontinuously confirmed in humans and only 5% of TD have associated with known null mice-related mutations (mainly PAX8 and TSHR). Notwithstanding, the advance in genetic testing represented by the next-generation sequencing (NGS) approach is steadily increasing the list of genes whose highly penetrant mutation predisposes to TD. In this review we intend to outline the molecular bases of TD, summarizing the current knowledge on thyroid development in both mice and humans and delineating the genetic features of its monogenetic forms. We will also highlight current strategies to enhance the insight into the non-Mendelian mechanisms of abnormal thyroid development.
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Affiliation(s)
- Catia Mio
- Department of Medicine, University of Udine, Udine, Italy
| | - Giorgio Grani
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Cosimo Durante
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Damante
- Department of Medicine, University of Udine, Udine, Italy.,Institute of Medical Genetics, Academic Hospital "Azienda Sanitaria Universitaria Integrata di Udine", Udine, Italy
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26
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Kravitz SN, Gregg C. New subtypes of allele-specific epigenetic effects: implications for brain development, function and disease. Curr Opin Neurobiol 2019; 59:69-78. [PMID: 31153086 DOI: 10.1016/j.conb.2019.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/24/2019] [Indexed: 01/15/2023]
Abstract
Typically, it is assumed that the maternal and paternal alleles for most genes are equally expressed. Known exceptions include canonical imprinted genes, random X-chromosome inactivation, olfactory receptors and clustered protocadherins. Here, we highlight recent studies showing that allele-specific expression is frequent in the genome and involves subtypes of epigenetic allelic effects that differ in terms of heritability, clonality and stability over time. Different forms of epigenetic allele regulation could have different roles in brain development, function, and disease. An emerging area involves understanding allelic effects in a cell-type and developmental stage-specific manner and determining how these effects influence the impact of genetic variants and mutations on the brain. A deeper understanding of epigenetics at the allele and cellular level in the brain could help clarify the mechanisms underlying phenotypic variance.
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Affiliation(s)
- Stephanie N Kravitz
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Christopher Gregg
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT 84132-3401, USA.
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27
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Reinius B, Sandberg R. Reply to 'High prevalence of clonal monoallelic expression'. Nat Genet 2019; 50:1199-1200. [PMID: 30082784 DOI: 10.1038/s41588-018-0189-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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28
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Vigneau S, Vinogradova S, Savova V, Gimelbrant A. High prevalence of clonal monoallelic expression. Nat Genet 2019; 50:1198-1199. [PMID: 30082785 DOI: 10.1038/s41588-018-0188-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Sébastien Vigneau
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Svetlana Vinogradova
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Virginia Savova
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander Gimelbrant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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29
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Nishino R, Petri S, Handel MA, Kunieda T, Fujiwara Y. Hybrid Sterility with Meiotic Metaphase Arrest in Intersubspecific Mouse Crosses. J Hered 2019; 110:183-193. [PMID: 30452700 PMCID: PMC6399516 DOI: 10.1093/jhered/esy060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/15/2018] [Indexed: 11/13/2022] Open
Abstract
Although organisms belonging to different species and subspecies sometimes produce fertile offspring, a hallmark of the speciation process is reproductive isolation, characterized by hybrid sterility (HS) due to failure in gametogenesis. In mammals, HS is usually exhibited by males, the heterogametic sex. The phenotypic manifestations of HS are complex. The most frequently observed are abnormalities in both autosomal and sex chromosome interactions that are linked to meiotic prophase arrest or postmeiotic spermiogenesis aberrations and lead to defective or absent gametes. The aim of this study was to determine the HS phenotypes in intersubspecific F1 mice produced by matings between Mus musculus molossinus-derived strains and diverse Mus musculus domesticus-inbred laboratory mouse strains. Most of these crosses produced fertile F1 offspring. However, when female BALB/cJ (domesticus) mice were mated to male JF1/MsJ (molossinus) mice, the (BALBdomxJF1mol)F1 males were sterile, whereas the (JF1molxBALBdom)F1 males produced by the reciprocal crossings were fertile; thus the sterility phenotype was asymmetric. The sterile (BALBdomxJF1mol) F1 males exhibited a high rate of meiotic metaphase arrest with misaligned chromosomes, probably related to a high frequency of XY dissociation. Intriguingly, in the sterile (BALBdomxJF1mol)F1 males we observed aberrant allele-specific expression of several meiotic genes, that play critical roles in important meiotic events including chromosome pairing. Together, these observations of an asymmetrical HS phenotype in intersubspecific F1 males, probably owing to meiotic defects in the meiotic behavior of the XY chromosomes pair and possibly also transcriptional misregulation of meiotic genes, provide new models and directions for understanding speciation mechanisms in mammals.
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Affiliation(s)
- Risako Nishino
- Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Okayama, Japan
- Institute of Environmental Toxicology, Joso, Ibaraki, Japan
| | | | | | - Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, Okayama, Japan
| | - Yasuhiro Fujiwara
- Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Okayama, Japan
- The Jackson Laboratory, Bar Harbor, ME, Japan
- Laboratory of Pathology and Development, Institute for Quantitative Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
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30
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Vinogradova S, Saksena SD, Ward HN, Vigneau S, Gimelbrant AA. MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin. BMC Bioinformatics 2019; 20:106. [PMID: 30819107 PMCID: PMC6394031 DOI: 10.1186/s12859-019-2679-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 02/13/2019] [Indexed: 01/13/2023] Open
Abstract
Background A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene expression that varies between clonal cell lineages. MAE is highly cell-type specific and mapping it in a large number of cell and tissue types can provide insight into its biological function. Its detection, however, remains challenging. Results We previously reported that a sequence-independent chromatin signature identifies, with high sensitivity and specificity, genes subject to MAE in multiple tissue types using readily available ChIP-seq data. Here we present an implementation of this method as a user-friendly, open-source software pipeline for monoallelic gene inference from chromatin (MaGIC). The source code for the MaGIC pipeline and the Shiny app is available at https://github.com/gimelbrantlab/magic. Conclusion The pipeline can be used by researchers to map monoallelic expression in a variety of cell types using existing models and to train new models with additional sets of chromatin marks. Electronic supplementary material The online version of this article (10.1186/s12859-019-2679-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Svetlana Vinogradova
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sachit D Saksena
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Henry N Ward
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,University of Minnesota-Twin Cities, Bioinformatics and Computational Biology Program, Minneapolis, MN, 55455, USA
| | - Sébastien Vigneau
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Alexander A Gimelbrant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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31
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Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. PLoS Genet 2019; 15:e1007874. [PMID: 30625149 PMCID: PMC6342324 DOI: 10.1371/journal.pgen.1007874] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/22/2019] [Accepted: 12/04/2018] [Indexed: 12/03/2022] Open
Abstract
Extensive cell-to-cell variation exists even among putatively identical cells, and there is great interest in understanding how the properties of transcription relate to this heterogeneity. Differential expression from the two gene copies in diploid cells could potentially contribute, yet our ability to measure from which gene copy individual RNAs originated remains limited, particularly in the context of tissues. Here, we demonstrate quantitative, single molecule allele-specific RNA FISH adapted for use on tissue sections, allowing us to determine the chromosome of origin of individual RNA molecules in formaldehyde-fixed tissues. We used this method to visualize the allele-specific expression of Xist and multiple autosomal genes in mouse kidney. By combining these data with mathematical modeling, we evaluated models for allele-specific heterogeneity, in particular demonstrating that apparent expression from only one of the alleles in single cells can arise as a consequence of low-level mRNA abundance and transcriptional bursting. In mammals, most cells of the body contain two genetic datasets: one from the mother and one from the father, and—in theory—these two sets of information could contribute equally to produce the molecules in a given cell. In practice, however, this is not always the case, which can have dramatic implications for many traits, including visible features (such as fur color) and even disease outcomes. However, it remains difficult to measure the parental origin of individual molecules in a given cell and thus to assess what processes lead to an imbalance of the maternal and paternal contribution. We adapted a microscopy technique—called allele-specific single molecule RNA FISH—that uses a combination of fluorescent tags to specifically label one type of molecule, RNA, depending on its origin, for use in mouse kidney sections. Focusing on RNAs that were previously reported to show imbalance, we performed measurements and combined these with mathematical modeling to quantify imbalance in tissues and explain how these can arise. We found that we could recapitulate the observed imbalances using models that only take into account the random processes that produce RNA, without the need to invoke special regulatory mechanisms to create unequal contributions.
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32
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Frequent monoallelic or skewed expression for developmental genes in CNS-derived cells and evidence for balancing selection. Proc Natl Acad Sci U S A 2018; 115:E10379-E10386. [PMID: 30322913 PMCID: PMC6217436 DOI: 10.1073/pnas.1808652115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cellular mosaicism due to monoallelic autosomal expression (MAE), with cell selection during development, is becoming increasingly recognized as prevalent in mammals, leading to interest in understanding its extent and mechanism(s). We report here use of clonal cell lines derived from the CNS of adult female [Formula: see text] hybrid (C57BL/6 X JF1) mice to characterize MAE as neural stem cells (nscs) differentiate to astrocyte-like cells (asls). We found that different subsets of genes show MAE in the two populations of cells; in each case, there is strong enrichment for genes specific to the respective developmental state. Genes that exhibit MAE are 22% of nsc-specific genes and 26% of asl-specific genes. Moreover, the promoters of genes with MAE have reduced CpG dinucleotides but increased CpG differences between the two parental mouse strains. Extending the study of variability to wild populations of mice, we found evidence for balancing selection as a contributing force in evolution of those genes showing developmental specificity (i.e., expressed in either nsc or asl), not just for genes showing MAE. Furthermore, we found that genes showing skewed allelic expression (SKE) were similarly enriched among cell type-specific genes and also showed a heightened probability of balancing selection. Thus, developmental stage-specific genes and genes with MAE or SKE seem to make up overlapping classes subject to selection for increased diversity. The implications of these results for development and evolution are discussed in the context of a model with stochastic epigenetic modifications taking place only during a relatively brief developmental window.
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33
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Epigenetic and Cellular Diversity in the Brain through Allele-Specific Effects. Trends Neurosci 2018; 41:925-937. [PMID: 30098802 DOI: 10.1016/j.tins.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 01/18/2023]
Abstract
The benefits of diploidy are considered to involve masking partially recessive mutations and increasing genetic diversity. Here, we review new studies showing evidence for diverse allele-specific expression and epigenetic states in mammalian brain cells, which suggest that diploidy expands the landscape of gene regulatory and expression programs in cells. Allele-specific expression has been thought to be restricted to a few specific classes of genes. However, new studies show novel genomic imprinting effects that are brain-region-, cell-type- and age-dependent. In addition, novel forms of random monoallelic expression that impact many autosomal genes have been described in vitro and in vivo. We discuss the implications for understanding the benefits of diploidy, and the mechanisms shaping brain development, function, and disease.
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34
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Integrated sequencing of exome and mRNA of large-sized single cells. Sci Rep 2018; 8:384. [PMID: 29321653 PMCID: PMC5762704 DOI: 10.1038/s41598-017-18730-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/16/2017] [Indexed: 11/08/2022] Open
Abstract
Current approaches of single cell DNA-RNA integrated sequencing are difficult to call SNPs, because a large amount of DNA and RNA is lost during DNA-RNA separation. Here, we performed simultaneous single-cell exome and transcriptome sequencing on individual mouse oocytes. Using microinjection, we kept the nuclei intact to avoid DNA loss, while retaining the cytoplasm inside the cell membrane, to maximize the amount of DNA and RNA captured from the single cell. We then conducted exome-sequencing on the isolated nuclei and mRNA-sequencing on the enucleated cytoplasm. For single oocytes, exome-seq can cover up to 92% of exome region with an average sequencing depth of 10+, while mRNA-sequencing reveals more than 10,000 expressed genes in enucleated cytoplasm, with similar performance for intact oocytes. This approach provides unprecedented opportunities to study DNA-RNA regulation, such as RNA editing at single nucleotide level in oocytes. In future, this method can also be applied to other large cells, including neurons, large dendritic cells and large tumour cells for integrated exome and transcriptome sequencing.
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35
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Abstract
Epigenetic mechanisms that cause maternally and paternally inherited alleles to be expressed differently in offspring have the potential to radically change our understanding of the mechanisms that shape disease susceptibility, phenotypic variation, cell fate, and gene expression. However, the nature and prevalence of these effects
in vivo have been unclear and are debated. Here, I consider major new studies of epigenetic allelic effects in cell lines and primary cells and
in vivo. The emerging picture is that these effects take on diverse forms, and this review attempts to clarify the nature of the different forms that have been uncovered for genomic imprinting and random monoallelic expression (RME). I also discuss apparent discrepancies between
in vitro and
in vivo studies. Importantly, multiple studies suggest that allelic effects are prevalent and can be developmental stage- and cell type-specific. I propose some possible functions and consider roles for allelic effects within the broader context of gene regulatory networks, cellular diversity, and plasticity. Overall, the field is ripe for discovery and is in need of mechanistic and functional studies.
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36
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Savova V, Vinogradova S, Pruss D, Gimelbrant AA, Weiss LA. Risk alleles of genes with monoallelic expression are enriched in gain-of-function variants and depleted in loss-of-function variants for neurodevelopmental disorders. Mol Psychiatry 2017; 22:1785-1794. [PMID: 28265118 PMCID: PMC5589474 DOI: 10.1038/mp.2017.13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 12/01/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023]
Abstract
Over 3000 human genes can be expressed from a single allele in one cell, and from the other allele-or both-in neighboring cells. Little is known about the consequences of this epigenetic phenomenon, monoallelic expression (MAE). We hypothesized that MAE increases expression variability, with a potential impact on human disease. Here, we use a chromatin signature to infer MAE for genes in lymphoblastoid cell lines and human fetal brain tissue. We confirm that across clones MAE status correlates with expression level, and that in human tissue data sets, MAE genes show increased expression variability. We then compare mono- and biallelic genes at three distinct scales. In the human population, we observe that genes with polymorphisms influencing expression variance are more likely to be MAE (P<1.1 × 10-6). At the trans-species level, we find gene expression differences and directional selection between humans and chimpanzees more common among MAE genes (P<0.05). Extending to human disease, we show that MAE genes are under-represented in neurodevelopmental copy number variants (CNVs) (P<2.2 × 10-10), suggesting that pathogenic variants acting via expression level are less likely to involve MAE genes. Using neuropsychiatric single-nucleotide polymorphism (SNP) and single-nucleotide variant (SNV) data, we see that genes with pathogenic expression-altering or loss-of-function variants are less likely MAE (P<7.5 × 10-11) and genes with only missense or gain-of-function variants are more likely MAE (P<1.4 × 10-6). Together, our results suggest that MAE genes tolerate a greater range of expression level than biallelic expression (BAE) genes, and this information may be useful in prediction of pathogenicity.
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Affiliation(s)
- V Savova
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - S Vinogradova
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - D Pruss
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - A A Gimelbrant
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - L A Weiss
- Department of Psychiatry and Institute for Human Genetics, University of California San Francisco, Langley Porter Psychiatric Institute, Nina Ireland Lab, San Francisco, CA, USA
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37
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Gui B, Slone J, Huang T. Perspective: Is Random Monoallelic Expression a Contributor to Phenotypic Variability of Autosomal Dominant Disorders? Front Genet 2017; 8:191. [PMID: 29250101 PMCID: PMC5718016 DOI: 10.3389/fgene.2017.00191] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/14/2017] [Indexed: 11/13/2022] Open
Abstract
Several factors have been proposed as contributors to interfamilial and intrafamilial phenotypic variability in autosomal dominant disorders, including allelic variation, modifier genes, environmental factors and complex genetic and environmental interactions. However, regardless of the similarity of genetic background and environmental factors, asymmetric limb or trunk anomalies in a single individual and variable manifestation between monozygotic twins have been observed, indicating other mechanisms possibly involved in expressivity of autosomal dominant diseases. One such example is Holt-Oram syndrome (HOS), which is characterized by congenital cardiac defects and forelimb anomalies, mainly attributed to mutations in the TBX5 gene. We hypothesize that monoallelic expression of the TBX5 gene occurs during embryo development, and, in the context of a mutation, random monoallelic expression (RME) can create discrepant functions in a proportion of cells and thus contribute to variable phenotypes. A hybrid mouse model was used to investigate the occurrence of RME with the Tbx5 gene, and single-cell reverse transcription PCR and restriction digestion were performed for limb bud cells from developing embryos (E11.5) of the hybrid mice. RME of Tbx5 was observed in approximately two-thirds of limb bud cells. These results indicate that RME of the Tbx5 gene occurs frequently during embryo development, resulting in a mosaic expression signature (monoallelic, biallelic, or null) that may provide a potential explanation for the widespread phenotypic variability in HOS. This model will further provide novel insights into the variability of autosomal dominant traits and a better understanding of the complex expressivity of disease conditions.
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Affiliation(s)
- Baoheng Gui
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jesse Slone
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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38
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Programming asynchronous replication in stem cells. Nat Struct Mol Biol 2017; 24:1132-1138. [PMID: 29131141 DOI: 10.1038/nsmb.3503] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 10/12/2017] [Indexed: 01/12/2023]
Abstract
Many regions of the genome replicate asynchronously and are expressed monoallelically. It is thought that asynchronous replication may be involved in choosing one allele over the other, but little is known about how these patterns are established during development. We show that, unlike somatic cells, which replicate in a clonal manner, embryonic and adult stem cells are programmed to undergo switching, such that daughter cells with an early-replicating paternal allele are derived from mother cells that have a late-replicating paternal allele. Furthermore, using ground-state embryonic stem (ES) cells, we demonstrate that in the initial transition to asynchronous replication, it is always the paternal allele that is chosen to replicate early, suggesting that primary allelic choice is directed by preset gametic DNA markers. Taken together, these studies help define a basic general strategy for establishing allelic discrimination and generating allelic diversity throughout the organism.
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39
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Zhao D, Lin M, Pedrosa E, Lachman HM, Zheng D. Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis. BMC Genomics 2017; 18:860. [PMID: 29126398 PMCID: PMC5681780 DOI: 10.1186/s12864-017-4261-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/01/2017] [Indexed: 12/24/2022] Open
Abstract
Background Monoallelic expression of autosomal genes has been implicated in human psychiatric disorders. However, there is a paucity of allelic expression studies in human brain cells at the single cell and genome wide levels. Results In this report, we reanalyzed a previously published single-cell RNA-seq dataset from several postmortem human brains and observed pervasive monoallelic expression in individual cells, largely in a random manner. Examining single nucleotide variants with a predicted functional disruption, we found that the “damaged” alleles were overall expressed in fewer brain cells than their counterparts, and at a lower level in cells where their expression was detected. We also identified many brain cell type-specific monoallelically expressed genes. Interestingly, many of these cell type-specific monoallelically expressed genes were enriched for functions important for those brain cell types. In addition, function analysis showed that genes displaying monoallelic expression and correlated expression across neuronal cells from different individual brains were implicated in the regulation of synaptic function. Conclusions Our findings suggest that monoallelic gene expression is prevalent in human brain cells, which may play a role in generating cellular identity and neuronal diversity and thus increasing the complexity and diversity of brain cell functions. Electronic supplementary material The online version of this article (10.1186/s12864-017-4261-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dejian Zhao
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA
| | - Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Present address: Department of Neuroscience, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu, 21166, China
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.,Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA
| | - Deyou Zheng
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA. .,Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA. .,Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, USA.
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40
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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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41
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Revealing allele-specific gene expression by single-cell transcriptomics. Int J Biochem Cell Biol 2017; 90:155-160. [PMID: 28578186 DOI: 10.1016/j.biocel.2017.05.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/21/2022]
Abstract
Single-cell sequencing has emerged as a revolutionary method that reveals biological processes with unprecedented resolution and scale, and has already greatly impacted biology and medicine. To investigate processes such as alternative splicing, novel exon detection and allele-specific expression (ASE), full-length based single-cell RNA-seq methods are required for broad sequence coverage and single nucleotide polymorphism (SNP) identification. In this review, we revisit recent achievements from studies that used single-cell RNA-seq to advance our understanding of ASE in the context of both autosomal and X-chromosome genes. We also recapitulate useful bioinformatic tools developed to identify haplotype phase.
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42
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Clonally stable Vκ allelic choice instructs Igκ repertoire. Nat Commun 2017; 8:15575. [PMID: 28555639 PMCID: PMC5459994 DOI: 10.1038/ncomms15575] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 04/07/2017] [Indexed: 12/30/2022] Open
Abstract
Although much has been done to understand how rearrangement of the Igκ locus is regulated during B-cell development, little is known about the way the variable (V) segments themselves are selected. Here we show, using B6/Cast hybrid pre-B-cell clones, that a limited number of V segments on each allele is stochastically activated as characterized by the appearance of non-coding RNA and histone modifications. The activation states are clonally distinct, stable across cell division and developmentally important in directing the Ig repertoire upon differentiation. Using a new approach of allelic ATAC-seq, we demonstrate that the Igκ V alleles have differential chromatin accessibility, which may serve as the underlying basis of clonal maintenance at this locus, as well as other instances of monoallelic expression throughout the genome. These findings highlight a new level of immune system regulation that optimizes gene diversity. B cell development involves sequential rearrangement of the immunoglobulin chains, but fine control over the selection process remains a mystery. Here the authors show that individual alleles in pre-B cells are clonally unique and result from stochastic activation of V gene segments to induce optimal generation of a diverse repertoire.
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43
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Sheinberger J, Hochberg H, Lavi E, Kanter I, Avivi S, Reinitz G, Schwed A, Aizler Y, Varon E, Kinor N, Shav-Tal Y. CD-tagging-MS2: detecting allelic expression of endogenous mRNAs and their protein products in single cells. Biol Methods Protoc 2017; 2:bpx004. [PMID: 32161787 PMCID: PMC6994078 DOI: 10.1093/biomethods/bpx004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/28/2017] [Accepted: 04/02/2017] [Indexed: 12/14/2022] Open
Abstract
Discriminating between the mRNA and protein outputs of each of the alleles of an endogenous gene in intact cells, is a difficult task. To examine endogenous transcripts originating from a specific allele, we applied Central Dogma tagging (CD-tagging), which is based on a tag insertion into an endogenous gene by creation of a new exon. Previously, CD-tagging was used to tag endogenous proteins. Here we developed a CD-tagging-MS2 approach in which two tags were inserted in tandem; a fluorescent protein tag in conjunction with the mRNA MS2 tag used for tagging mRNAs in cells. A cell clone library of CD-tagged-MS2 genes was generated, and protein and mRNA distributions were examined and characterized in single cells. Taking advantage of having one allele tagged, we demonstrate how the transcriptional activity of all alleles, tagged and untagged, can be identified using single molecule RNA fluorescence in situ hybridization (smFISH). Allele-specific mRNA expression and localization were quantified under normal and stress conditions. The latter generate cytoplasmic stress granules (SGs) that can store mRNAs, and the distribution of the mRNAs within and outside of the SGs was measured. Altogether, CD-tagging-MS2 is a robust and inexpensive approach for direct simultaneous detection of an endogenous mRNA and its translated protein product in the same cell.
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Affiliation(s)
- Jonathan Sheinberger
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Hodaya Hochberg
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Erez Lavi
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Itamar Kanter
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Shira Avivi
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Gita Reinitz
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Avital Schwed
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Yuval Aizler
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eli Varon
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Noa Kinor
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, 5290002, Israel
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Abstract
Monoallelic expression not due to cis-regulatory sequence polymorphism poses an intriguing problem in epigenetics because it requires the unequal treatment of two segments of DNA that are present in the same nucleus and that can indeed have absolutely identical sequences. Here, I focus on a few recent developments in the field of monoallelic expression that are of particular interest and raise interesting questions for future work. One development is regarding analyses of imprinted genes, in which recent work suggests the possibility that intriguing networks of imprinted genes exist and are important for genetic and physiological studies. Another issue that has been raised in recent years by a number of publications is the question of how skewed allelic expression should be for it to be designated as monoallelic expression and, further, what methods are appropriate or inappropriate for analyzing genomic data to examine allele-specific expression. Perhaps the most exciting recent development in mammalian monoallelic expression is a clever and carefully executed analysis of genetic diversity of autosomal genes subject to random monoallelic expression (RMAE), which provides compelling evidence for distinct evolutionary forces acting on random monoallelically expressed genes.
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Affiliation(s)
- Andrew Chess
- Department of Genetics and Genomic Sciences, Department of Developmental and Regenerative Biology, Fishberg Department of Neuroscience, and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574;
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45
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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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46
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Liu T, Li H, Ding Y, Qi Y, Gao Y, Song A, Shen J, Qiu L. Genome-wide gene expression patterns in dikaryon of the basidiomycete fungus Pleurotus ostreatus. Braz J Microbiol 2017; 48:380-390. [PMID: 28089161 PMCID: PMC5470450 DOI: 10.1016/j.bjm.2016.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/20/2016] [Indexed: 01/10/2023] Open
Abstract
Dikarya is a subkingdom of fungi that includes Ascomycota and Basidiomycota. The gene expression patterns of dikaryon are poorly understood. In this study, we bred a dikaryon DK13×3 by mating monokaryons MK13 and MK3, which were from the basidiospores of Pleurotus ostreatus TD300. Using RNA-Seq, we obtained the transcriptomes of the three strains. We found that the total transcript numbers in the transcriptomes of the three strains were all more than ten thousand, and the expression profile in DK13×3 was more similar to MK13 than MK3. However, the genes involved in macromolecule utilization, cellular material synthesis, stress-resistance and signal transduction were much more up-regulated in the dikaryon than its constituent monokaryons. All possible modes of differential gene expression, when compared to constituent monokaryons, including the presence/absence variation, and additivity/nonadditivity gene expression in the dikaryon may contribute to heterosis. By sequencing the urease gene poure sequences and mRNA sequences, we identified the monoallelic expression of the poure gene in the dikaryon, and its transcript was from the parental monokaryon MK13. Furthermore, we discovered RNA editing in the poure gene mRNA of the three strains. These results suggest that the gene expression patterns in dikaryons should be similar to that of diploids during vegetative growth.
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Affiliation(s)
- Tianxiang Liu
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Huiru Li
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Yatong Ding
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Yuancheng Qi
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Yuqian Gao
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Andong Song
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Jinwen Shen
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Liyou Qiu
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China.
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47
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Jeffries AR, Uwanogho DA, Cocks G, Perfect LW, Dempster E, Mill J, Price J. Erasure and reestablishment of random allelic expression imbalance after epigenetic reprogramming. RNA (NEW YORK, N.Y.) 2016; 22:1620-1630. [PMID: 27539784 PMCID: PMC5029458 DOI: 10.1261/rna.058347.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Clonal level random allelic expression imbalance and random monoallelic expression provides cellular heterogeneity within tissues by modulating allelic dosage. Although such expression patterns have been observed in multiple cell types, little is known about when in development these stochastic allelic choices are made. We examine allelic expression patterns in human neural progenitor cells before and after epigenetic reprogramming to induced pluripotency, observing that loci previously characterized by random allelic expression imbalance (0.63% of expressed genes) are generally reset to a biallelic state in induced pluripotent stem cells (iPSCs). We subsequently neuralized the iPSCs and profiled isolated clonal neural stem cells, observing that significant random allelic expression imbalance is reestablished at 0.65% of expressed genes, including novel loci not found to show allelic expression imbalance in the original parental neural progenitor cells. Allelic expression imbalance was associated with altered DNA methylation across promoter regulatory regions, with clones characterized by skewed allelic expression being hypermethylated compared to their biallelic sister clones. Our results suggest that random allelic expression imbalance is established during lineage commitment and is associated with increased DNA methylation at the gene promoter.
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Affiliation(s)
- Aaron Richard Jeffries
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Dafe Aghogho Uwanogho
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Graham Cocks
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Leo William Perfect
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Emma Dempster
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Jack Price
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
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48
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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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49
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Yeo S, Hodgkinson CA, Zhou Z, Jung J, Leung M, Yuan Q, Goldman D. The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits. BMC Genomics 2016; 17:620. [PMID: 27515598 PMCID: PMC4982227 DOI: 10.1186/s12864-016-2922-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/07/2016] [Indexed: 12/16/2022] Open
Abstract
Background Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL’s for complex phenotypes. Results We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. Additionally several novel DAE-QTLs not identified as cis-eQTLs were identified suggesting that there are differences in sensitivity and specificity for QTL detection between the two methodologies. Strain specific DAE QTLs in B6/DBAF1 mice were located in excess at candidate genes for alcohol use disorders, seizures, and angiogenesis previously implicated by genetic linkage in C57BL/6J × DBA/2JF2 mice or BXD RI strains. Conclusions Via a survey for differential allele expression in F1 mice, a substantial proportion of genes were found to have alleles altering expression in cis-acting fashion. Comparing forebrain and kidney, many or most of these alleles were tissue-specific in action. The identification of strain specific DAE QTLs, can assist in assessment of candidate genes located within the large intervals associated with trait QTLs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2922-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seungeun Yeo
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Colin A Hodgkinson
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Zhifeng Zhou
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Jeesun Jung
- Laboratory of Epidemiology and Biometry, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Ming Leung
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Qiaoping Yuan
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA
| | - David Goldman
- Laboratory of Neurogenetics, National institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, 20852, USA.
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50
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Magne F, Ge B, Larrivée-Vanier S, Van Vliet G, Samuels ME, Pastinen T, Deladoëy J. Demonstration of Autosomal Monoallelic Expression in Thyroid Tissue Assessed by Whole-Exome and Bulk RNA Sequencing. Thyroid 2016; 26:852-9. [PMID: 27125219 DOI: 10.1089/thy.2016.0009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Congenital hypothyroidism due to thyroid dysgenesis (CHTD) is a disorder with a prevalence of 1/4000 live births, the cause of which remains unknown. The most common diagnostic category is thyroid ectopy, which occurs in up to 80% of CHTD cases. CHTD is predominantly not inherited and has a high discordance rate (>92%) between monozygotic (MZ) twins. The sporadic nature of CHTD might be explained by somatic events such as autosomal monoallelic expression (AME), given that genes expressed in a monoallelic way are more vulnerable to otherwise benign monoallelict genetic or epigenetic mutations. OBJECTIVE The aim of this study was to search for complete (90%) AME in normal and dysgenetic thyroid tissues. METHODS Aggregated analysis of whole-exome and bulk RNA sequencing was performed on two ectopic thyroids, four normal thyroids, and the human thyroid cell line Nthy-ori. RESULTS A median of 5062 (range 2081-5270) genes per sample showed sufficient numbers of heterozygous single nucleotide polymorphisms to be informative. The median monoallelic expression represented 22 (range 16-32) of the informative genes for each thyroid sample. Examples of genes displaying AME are FCGBP, ZNF331, USP10, BCLAF1, and some HLA genes; these genes are involved in epithelial-mesenchymal transition, cell migration, cancer, and immunity. CONCLUSIONS AME may account for the high discordance rate observed between MZ twins and for the sporadic nature of CHTD. These findings also have implications for other pathologies, including cancers and autoimmune disorders of the thyroid.
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Affiliation(s)
- Fabien Magne
- 1 Endocrinology Service and Research Center, Sainte-Justine University Hospital Center, Department of Pediatrics, Université de Montréal , Montreal, Canada
- 2 Department of Biomedical Sciences, Université de Montréal , Montreal, Canada
| | - Bing Ge
- 3 Department of Human Genetics, McGill University , Montreal, Canada
| | - Stéphanie Larrivée-Vanier
- 1 Endocrinology Service and Research Center, Sainte-Justine University Hospital Center, Department of Pediatrics, Université de Montréal , Montreal, Canada
| | - Guy Van Vliet
- 1 Endocrinology Service and Research Center, Sainte-Justine University Hospital Center, Department of Pediatrics, Université de Montréal , Montreal, Canada
| | - Mark E Samuels
- 1 Endocrinology Service and Research Center, Sainte-Justine University Hospital Center, Department of Pediatrics, Université de Montréal , Montreal, Canada
- 4 Department of Medicine, Université de Montréal , Montreal, Canada
| | - Tomi Pastinen
- 3 Department of Human Genetics, McGill University , Montreal, Canada
| | - Johnny Deladoëy
- 1 Endocrinology Service and Research Center, Sainte-Justine University Hospital Center, Department of Pediatrics, Université de Montréal , Montreal, Canada
- 2 Department of Biomedical Sciences, Université de Montréal , Montreal, Canada
- 5 Department of Biochemistry, Université de Montréal , Montreal, Canada
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