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Sacristán C, Youngblood BA, Lu P, Bally APR, Xu JX, McGary K, Hewitt SL, Boss JM, Skok JA, Ahmed R, Dustin ML. Chronic viral infection alters PD-1 locus subnuclear localization in cytotoxic CD8 + T cells. Cell Rep 2024; 43:114547. [PMID: 39083377 DOI: 10.1016/j.celrep.2024.114547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/15/2024] [Accepted: 07/11/2024] [Indexed: 08/02/2024] Open
Abstract
During chronic infection, virus-specific CD8+ cytotoxic T lymphocytes (CTLs) progressively lose their ability to mount effective antiviral responses. This "exhaustion" is coupled to persistent upregulation of inhibitory receptor programmed death-1 (PD-1) (Pdcd1)-key in suppressing antiviral CTL responses. Here, we investigate allelic Pdcd1 subnuclear localization and transcription during acute and chronic lymphocytic choriomeningitis virus (LCMV) infection in mice. Pdcd1 alleles dissociate from transcriptionally repressive chromatin domains (lamin B) in virus-specific exhausted CTLs but not in naive or effector CTLs. Relative to naive CTLs, nuclear positioning and Pdcd1-lamina dissociation in exhausted CTLs reflect loss of Pdcd1 promoter methylation and greater PD-1 upregulation, although a direct correlation is not observed in effector cells, 8 days post-infection. Genetic deletion of B lymphocyte-induced maturation protein 1 (Blimp-1) enhances Pdcd1-lamina dissociation in effector CTLs, suggesting that Blimp-1 contributes to maintaining Pdcd1 localization to repressive lamina. Our results identify mechanisms governing Pdcd1 subnuclear localization and the broader role of chromatin dynamics in T cell exhaustion.
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Affiliation(s)
- Catarina Sacristán
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Ben A Youngblood
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA; Immunology Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Peiyuan Lu
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Alexander P R Bally
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Jean Xiaojin Xu
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Katelyn McGary
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Susannah L Hewitt
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Jeremy M Boss
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Rafi Ahmed
- Emory Vaccine Center and the Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Michael L Dustin
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA; The Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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2
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Sands B, Yun SR, Oshima J, Mendenhall AR. Maternal histone methyltransferases antagonistically regulate monoallelic expression in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576748. [PMID: 38328214 PMCID: PMC10849558 DOI: 10.1101/2024.01.22.576748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Undefined epigenetic programs act to probabilistically silence individual autosomal alleles, generating unique individuals, even from genetic clones. This sort of random monoallelic expression can explain variation in traits and diseases that differences in genes and environments cannot. Here, we developed the nematode Caenorhabditis elegans to study monoallelic expression in whole tissues, and defined a developmental genetic regulation pathway. We found maternal H3K9 histone methyltransferase (HMT) SET-25/SUV39/G9a works with HPL-2/HP1 and LIN-61/L3MBTL2 to randomly silence alleles in the intestinal progenitor E-cell of 8-cell embryos to cause monoallelic expression. SET-25 was antagonized by another maternal H3K9 HMT, MET-2/SETDB1, which works with LIN-65/ATF7ZIP and ARLE-14/ARL14EP to prevent monoallelic expression. The HMT-catalytic SET domains of both MET-2 and SET-25 were required for regulating monoallelic expression. Our data support a model wherein SET-25 and MET-2 regulate histones during development to generate patterns of somatic monoallelic expression that are persistent but not heritable.
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3
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Ballouz S, Kawaguchi RK, Pena MT, Fischer S, Crow M, French L, Knight FM, Adams LB, Gillis J. The transcriptional legacy of developmental stochasticity. Nat Commun 2023; 14:7226. [PMID: 37940702 PMCID: PMC10632366 DOI: 10.1038/s41467-023-43024-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Genetic and environmental variation are key contributors during organism development, but the influence of minor perturbations or noise is difficult to assess. This study focuses on the stochastic variation in allele-specific expression that persists through cell divisions in the nine-banded armadillo (Dasypus novemcinctus). We investigated the blood transcriptome of five wild monozygotic quadruplets over time to explore the influence of developmental stochasticity on gene expression. We identify an enduring signal of autosomal allelic variability that distinguishes individuals within a quadruplet despite their genetic similarity. This stochastic allelic variation, akin to X-inactivation but broader, provides insight into non-genetic influences on phenotype. The presence of stochastically canalized allelic signatures represents a novel axis for characterizing organismal variability, complementing traditional approaches based on genetic and environmental factors. We also developed a model to explain the inconsistent penetrance associated with these stochastically canalized allelic expressions. By elucidating mechanisms underlying the persistence of allele-specific expression, we enhance understanding of development's role in shaping organismal diversity.
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Affiliation(s)
- Sara Ballouz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Risa Karakida Kawaguchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Maria T Pena
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare System Bureau, National Hansen's Disease Program, Baton Rouge, LA, 70803, USA
| | - Stephan Fischer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, F-75015, France
| | - Megan Crow
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Genentech, Inc., South San Francisco, CA, USA
| | - Leon French
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | | | - Linda B Adams
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare System Bureau, National Hansen's Disease Program, Baton Rouge, LA, 70803, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
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4
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Shayota BJ. Downstream Assays for Variant Resolution: Epigenetics, RNA Sequnncing, and Metabolomics. Pediatr Clin North Am 2023; 70:929-936. [PMID: 37704351 DOI: 10.1016/j.pcl.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
As the availability of advanced molecular testing like whole exome and genome sequencing expands, it comes with the added complication of interpreting inconclusive results, including determining the relevance of variants of uncertain significance or failing to find a variant in an otherwise suspected specific genetic disorder. This complication necessitates the use of alternative testing methods to gather more information in support of, or against, a particular genetic diagnosis. Therefore, new genome-wide approaches, including DNA epigenetic testing, RNA sequencing, and metabolomics, are increasingly being used to increase the diagnostic yield when used in conjunction with more conventional genetic tests.
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Affiliation(s)
- Brian J Shayota
- University of Utah, 295 Chipeta Way, Salt Lake City, UT 84108, USA; Primary Children's Hospital, Salt Lake City, UT, USA.
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5
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Balasooriya GI, Spector DL. Allele pairing at Sun1-enriched domains at the nuclear periphery via T1A3 tandem DNA repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536031. [PMID: 37066204 PMCID: PMC10104147 DOI: 10.1101/2023.04.07.536031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Spatiotemporal gene regulation is fundamental to the biology of diploid cells. Therefore, effective communication between two alleles and their geometry in the nucleus is important. However, the mechanism that fine-tunes the expression from each of the two alleles of an autosome is enigmatic. Establishing an allele-specific gene expression visualization system in living cells, we show that alleles of biallelically expressed Cth and Ttc4 genes are paired prior to acquiring monoallelic expression. We found that active alleles of monoallelic genes are preferentially localized at Sun1-enriched domains at the nuclear periphery. These peripherally localized active DNA loci are enriched with adenine-thymidine-rich tandem repeats that interact with Hnrnpd and reside in a Hi-C-defined A compartment within the B compartment. Our results demonstrate the biological significance of T 1 A 3 tandem repeat sequences in genome organization and how the regulation of gene expression, at the level of individual alleles, relates to their spatial arrangement.
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6
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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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7
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Vihinen M. Individual Genetic Heterogeneity. Genes (Basel) 2022; 13:genes13091626. [PMID: 36140794 PMCID: PMC9498725 DOI: 10.3390/genes13091626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22184 Lund, Sweden
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8
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Targeted Long-Read Bisulfite Sequencing Identifies Differences in the TERT Promoter Methylation Profiles between TERT Wild-Type and TERT Mutant Cancer Cells. Cancers (Basel) 2022; 14:cancers14164018. [PMID: 36011010 PMCID: PMC9406525 DOI: 10.3390/cancers14164018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/06/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Background: TERT promoter methylation, located several hundred base pairs upstream of the transcriptional start site, is cancer specific and correlates with increased TERT mRNA expression and poorer patient outcome. Promoter methylation, however, is not mutually exclusive to TERT activating genetic alterations, as predicted for functionally redundant mechanisms. To annotate the altered patterns of TERT promoter methylation and their relationship with gene expression, we applied a Pacific Biosciences-based, long-read, bisulfite-sequencing technology and compared the differences in the methylation marks between wild-type and mutant cancers in an allele-specific manner. Results: We cataloged TERT genetic alterations (i.e., promoter point mutations or structural variations), allele-specific promoter methylation patterns, and allele-specific expression levels in a cohort of 54 cancer cell lines. In heterozygous mutant cell lines, the mutant alleles were significantly less methylated than their silent, mutation-free alleles (p < 0.05). In wild-type cell lines, by contrast, both epialleles were equally methylated to high levels at the TERT distal promoter, but differentially methylated in the proximal regions. ChIP analysis showed that epialleles with the hypomethylated proximal and core promoter were enriched in the active histone mark H3K4me2/3, whereas epialleles that were methylated in those regions were enriched in the repressive histone mark H3K27me3. Decitabine therapy induced biallelic expression in the wild-type cancer cells, whereas the mutant cell lines were unaffected. Conclusions: Long-read bisulfite sequencing analysis revealed differences in the methylation profiles and responses to demethylating agents between TERT wild-type and genetically altered cancer cell lines. The causal relation between TERT promoter methylation and gene expression remains to be established.
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9
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Kissiov DU, Ethell A, Chen S, Wolf NK, Zhang C, Dang SM, Jo Y, Madsen KN, Paranjpe I, Lee AY, Chim B, Muljo SA, Raulet DH. Binary outcomes of enhancer activity underlie stable random monoallelic expression. eLife 2022; 11:e74204. [PMID: 35617021 PMCID: PMC9135403 DOI: 10.7554/elife.74204] [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: 09/24/2021] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Mitotically stable random monoallelic gene expression (RME) is documented for a small percentage of autosomal genes. We developed an in vivo genetic model to study the role of enhancers in RME using high-resolution single-cell analysis of natural killer (NK) cell receptor gene expression and enhancer deletions in the mouse germline. Enhancers of the RME NK receptor genes were accessible and enriched in H3K27ac on silent and active alleles alike in cells sorted according to allelic expression status, suggesting enhancer activation and gene expression status can be decoupled. In genes with multiple enhancers, enhancer deletion reduced gene expression frequency, in one instance converting the universally expressed gene encoding NKG2D into an RME gene, recapitulating all aspects of natural RME including mitotic stability of both the active and silent states. The results support the binary model of enhancer action, and suggest that RME is a consequence of general properties of gene regulation by enhancers rather than an RME-specific epigenetic program. Therefore, many and perhaps all genes may be subject to some degree of RME. Surprisingly, this was borne out by analysis of several genes that define different major hematopoietic lineages, that were previously thought to be universally expressed within those lineages: the genes encoding NKG2D, CD45, CD8α, and Thy-1. We propose that intrinsically probabilistic gene allele regulation is a general property of enhancer-controlled gene expression, with previously documented RME representing an extreme on a broad continuum.
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Affiliation(s)
- Djem U Kissiov
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Alexander Ethell
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sean Chen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Natalie K Wolf
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Chenyu Zhang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Susanna M Dang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Yeara Jo
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Katrine N Madsen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Ishan Paranjpe
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Angus Y Lee
- Cancer Research Laboratory, University of California, BerkeleyBerkeleyUnited States
| | - Bryan Chim
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Stefan A Muljo
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - David H Raulet
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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10
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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: 4] [Impact Index Per Article: 2.0] [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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11
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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12
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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: 5] [Impact Index Per Article: 1.7] [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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13
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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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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: 5] [Impact Index Per Article: 1.7] [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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15
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Mompart F, Kamgoué A, Lahbib-Mansais Y, Robelin D, Bonnet A, Rogel-Gaillard C, Kocanova S, Yerle-Bouissou M. The 3D nuclear conformation of the major histocompatibility complex changes upon cell activation both in porcine and human macrophages. BMC Mol Cell Biol 2021; 22:45. [PMID: 34521351 PMCID: PMC8442435 DOI: 10.1186/s12860-021-00384-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The crucial role of the major histocompatibility complex (MHC) for the immune response to infectious diseases is well-known, but no information is available on the 3D nuclear organization of this gene-dense region in immune cells, whereas nuclear architecture is known to play an essential role on genome function regulation. We analyzed the spatial arrangement of the three MHC regions (class I, III and II) in macrophages using 3D-FISH. Since this complex presents major differences in humans and pigs with, notably, the presence of the centromere between class III and class II regions in pigs, the analysis was implemented in both species to determine the impact of this organization on the 3D conformation of the MHC. The expression level of the three genes selected to represent each MHC region was assessed by quantitative real-time PCR. Resting and lipopolysaccharide (LPS)-activated states were investigated to ascertain whether a response to a pathogen modifies their expression level and their 3D organization. RESULTS While the three MHC regions occupy an intermediate radial position in porcine macrophages, the class I region was clearly more peripheral in humans. The BAC center-to-center distances allowed us to propose a 3D nuclear organization of the MHC in each species. LPS/IFNγ activation induces a significant decompaction of the chromatin between class I and class III regions in pigs and between class I and class II regions in humans. We detected a strong overexpression of TNFα (class III region) in both species. Moreover, a single nucleus analysis revealed that the two alleles can have either the same or a different compaction pattern. In addition, macrophage activation leads to an increase in alleles that present a decompacted pattern in humans and pigs. CONCLUSIONS The data presented demonstrate that: (i) the MHC harbors a different 3D organization in humans and pigs; (ii) LPS/IFNγ activation induces chromatin decompaction, but it is not the same area affected in the two species. These findings were supported by the application of an original computation method based on the geometrical distribution of the three target genes. Finally, the position of the centromere inside the swine MHC could influence chromatin reorganization during the activation process.
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Affiliation(s)
- Florence Mompart
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | - Alain Kamgoué
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Yvette Lahbib-Mansais
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | - David Robelin
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | - Agnès Bonnet
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | | | - Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Martine Yerle-Bouissou
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France.
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Shah A, Ratkowski M, Rosa A, Feinstein P, Bozza T. Olfactory expression of trace amine-associated receptors requires cooperative cis-acting enhancers. Nat Commun 2021; 12:3797. [PMID: 34145232 PMCID: PMC8213819 DOI: 10.1038/s41467-021-23824-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 05/18/2021] [Indexed: 11/28/2022] Open
Abstract
Olfactory sensory neurons express a large family of odorant receptors (ORs) and a small family of trace amine-associated receptors (TAARs). While both families are subject to so-called singular expression (expression of one allele of one gene), the mechanisms underlying TAAR gene choice remain obscure. Here, we report the identification of two conserved sequence elements in the mouse TAAR cluster (T-elements) that are required for TAAR gene expression. We observed that cell-type-specific expression of a TAAR-derived transgene required either T-element. Moreover, deleting either element reduced or abolished expression of a subset of TAAR genes, while deleting both elements abolished olfactory expression of all TAARs in cis with the mutation. The T-elements exhibit several features of known OR enhancers but also contain highly conserved, unique sequence motifs. Our data demonstrate that TAAR gene expression requires two cooperative cis-acting enhancers and suggest that ORs and TAARs share similar mechanisms of singular expression.
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Affiliation(s)
- Ami Shah
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Madison Ratkowski
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Alessandro Rosa
- The Graduate Center Programs in Biochemistry, Biology and CUNY Neuroscience Collaborative, New York, NY, USA
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Paul Feinstein
- The Graduate Center Programs in Biochemistry, Biology and CUNY Neuroscience Collaborative, New York, NY, USA
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Thomas Bozza
- Department of Neurobiology, Northwestern University, Evanston, IL, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
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Ah‐Fong AM, Boyd AM, Matson ME, Judelson HS. A Cas12a-based gene editing system for Phytophthora infestans reveals monoallelic expression of an elicitor. MOLECULAR PLANT PATHOLOGY 2021; 22:737-752. [PMID: 33724663 PMCID: PMC8126191 DOI: 10.1111/mpp.13051] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 05/03/2023]
Abstract
Phytophthora infestans is a destructive pathogen of potato and a model for investigations of oomycete biology. The successful application of a CRISPR gene editing system to P. infestans is so far unreported. We discovered that it is difficult to express CRISPR/Cas9 but not a catalytically inactive form in transformants, suggesting that the active nuclease is toxic. We were able to achieve editing with CRISPR/Cas12a using vectors in which the nuclease and its guide RNA were expressed from a single transcript. Using the elicitor gene Inf1 as a target, we observed editing of one or both alleles in up to 13% of transformants. Editing was more efficient when guide RNA processing relied on the Cas12a direct repeat instead of ribozyme sequences. INF1 protein was not made when both alleles were edited in the same transformant, but surprisingly also when only one allele was altered. We discovered that the isolate used for editing, 1306, exhibited monoallelic expression of Inf1 due to insertion of a copia-like element in the promoter of one allele. The element exhibits features of active retrotransposons, including a target site duplication, long terminal repeats, and an intact polyprotein reading frame. Editing occurred more often on the transcribed allele, presumably due to differences in chromatin structure. The Cas12a system not only provides a tool for modifying genes in P. infestans, but also for other members of the genus by expanding the number of editable sites. Our work also highlights a natural mechanism that remodels oomycete genomes.
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Affiliation(s)
- Audrey M.V. Ah‐Fong
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Amy M. Boyd
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Michael E.H. Matson
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Howard S. Judelson
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCaliforniaUSA
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18
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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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Aslam MA, Alemdehy MF, Hao B, Krijger PHL, Pritchard CEJ, de Rink I, Muhaimin FI, Nurzijah I, van Baalen M, Kerkhoven RM, van den Berk PCM, Skok JA, Jacobs H. The Ig heavy chain protein but not its message controls early B cell development. Proc Natl Acad Sci U S A 2020; 117:31343-31352. [PMID: 33229554 PMCID: PMC7733823 DOI: 10.1073/pnas.2004810117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Development of progenitor B cells (ProB cells) into precursor B cells (PreB cells) is dictated by immunoglobulin heavy chain checkpoint (IgHCC), where the IgHC encoded by a productively rearranged Igh allele assembles into a PreB cell receptor complex (PreBCR) to generate signals to initiate this transition and suppressing antigen receptor gene recombination, ensuring that only one productive Igh allele is expressed, a phenomenon known as Igh allelic exclusion. In contrast to a productively rearranged Igh allele, the Igh messenger RNA (mRNA) (IgHR) from a nonproductively rearranged Igh allele is degraded by nonsense-mediated decay (NMD). This fact prohibited firm conclusions regarding the contribution of stable IgHR to the molecular and developmental changes associated with the IgHCC. This point was addressed by generating the IghTer5H∆TM mouse model from IghTer5H mice having a premature termination codon at position +5 in leader exon of IghTer5H allele. This prohibited NMD, and the lack of a transmembrane region (∆TM) prevented the formation of any signaling-competent PreBCR complexes that may arise as a result of read-through translation across premature Ter5 stop codon. A highly sensitive sandwich Western blot revealed read-through translation of IghTer5H message, indicating that previous conclusions regarding a role of IgHR in establishing allelic exclusion requires further exploration. As determined by RNA sequencing (RNA-Seq), this low amount of IgHC sufficed to initiate PreB cell markers normally associated with PreBCR signaling. In contrast, the IghTer5H∆TM knock-in allele, which generated stable IgHR but no detectable IgHC, failed to induce PreB development. Our data indicate that the IgHCC is controlled at the level of IgHC and not IgHR expression.
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Affiliation(s)
- Muhammad Assad Aslam
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, 60800 Multan, Pakistan
| | - Mir Farshid Alemdehy
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Bingtao Hao
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Peter H L Krijger
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Colin E J Pritchard
- Mouse Clinic for Cancer and Aging Transgenic Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Iris de Rink
- Genome Core Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | | | - Ika Nurzijah
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Martijn van Baalen
- Flow Cytometry Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ron M Kerkhoven
- Genome Core Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Paul C M van den Berk
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
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20
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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: 9] [Impact Index Per Article: 2.3] [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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21
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Vihinen M. Functional effects of protein variants. Biochimie 2020; 180:104-120. [PMID: 33164889 DOI: 10.1016/j.biochi.2020.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
Abstract
Genetic and other variations frequently affect protein functions. Scientific articles can contain confusing descriptions about which function or property is affected, and in many cases the statements are pure speculation without any experimental evidence. To clarify functional effects of protein variations of genetic or non-genetic origin, a systematic conceptualisation and framework are introduced. This framework describes protein functional effects on abundance, activity, specificity and affinity, along with countermeasures, which allow cells, tissues and organisms to tolerate, avoid, repair, attenuate or resist (TARAR) the effects. Effects on abundance discussed include gene dosage, restricted expression, mis-localisation and degradation. Enzymopathies, effects on kinetics, allostery and regulation of protein activity are subtopics for the effects of variants on activity. Variation outcomes on specificity and affinity comprise promiscuity, specificity, affinity and moonlighting. TARAR mechanisms redress variations with active and passive processes including chaperones, redundancy, robustness, canalisation and metabolic and signalling rewiring. A framework for pragmatic protein function analysis and presentation is introduced. All of the mechanisms and effects are described along with representative examples, most often in relation to diseases. In addition, protein function is discussed from evolutionary point of view. Application of the presented framework facilitates unambiguous, detailed and specific description of functional effects and their systematic study.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22 184, Lund, Sweden.
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22
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Vohra M, Sharma AR, Prabhu B N, Rai PS. SNPs in Sites for DNA Methylation, Transcription Factor Binding, and miRNA Targets Leading to Allele-Specific Gene Expression and Contributing to Complex Disease Risk: A Systematic Review. Public Health Genomics 2020; 23:155-170. [PMID: 32966991 DOI: 10.1159/000510253] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/16/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION The complex genetic diversity among human populations results from an assortment of factors acting at various sequential levels, including mutations, population migrations, genetic drift, and selection. Although there are a plethora of DNA sequence variations identified through genome-wide association studies (GWAS), the challenge remains to explain the mechanisms underlying interindividual phenotypic disparity accounting for disease susceptibility. Single nucleotide polymorphisms (SNPs) present in the sites for DNA methylation, transcription factor (TF) binding, or miRNA targets can alter the gene expression. The systematic review aimed to evaluate the complex crosstalk among SNPs, miRNAs, DNA methylation, and TFs for complex multifactorial disease risk. METHODS PubMed and Scopus databases were used from inception until May 15, 2019. Initially, screening of articles involved studies assessing the interaction of SNPs with TFs, DNA methylation, or miRNAs resulting in allele-specific gene expression in complex multifactorial diseases. We also included the studies which provided experimental validation of the interaction of SNPs with each of these factors. The results from various studies on multifactorial diseases were assessed. RESULTS A total of 11 articles for SNPs interacting with DNA methylation, 30 articles for SNPs interacting with TFs, and 11 articles for SNPs in miRNA binding sites were selected. The interactions of SNPs with epigenetic factors were found to be implicated in different types of cancers, autoimmune diseases, cardiovascular diseases, diabetes, and asthma. CONCLUSION The systematic review provides evidence for the interplay between genetic and epigenetic risk factors through allele-specific gene expression in various complex multifactorial diseases.
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Affiliation(s)
- Manik Vohra
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Anu Radha Sharma
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Navya Prabhu B
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Padmalatha S Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India,
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Aeby E, Lee HG, Lee YW, Kriz A, del Rosario BC, Oh HJ, Boukhali M, Haas W, Lee JT. Decapping enzyme 1A breaks X-chromosome symmetry by controlling Tsix elongation and RNA turnover. Nat Cell Biol 2020; 22:1116-1129. [PMID: 32807903 DOI: 10.1038/s41556-020-0558-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/09/2020] [Indexed: 12/27/2022]
Abstract
How allelic asymmetry is generated remains a major unsolved problem in epigenetics. Here we model the problem using X-chromosome inactivation by developing "BioRBP", an enzymatic RNA-proteomic method that enables probing of low-abundance interactions and an allelic RNA-depletion and -tagging system. We identify messenger RNA-decapping enzyme 1A (DCP1A) as a key regulator of Tsix, a noncoding RNA implicated in allelic choice through X-chromosome pairing. DCP1A controls Tsix half-life and transcription elongation. Depleting DCP1A causes accumulation of X-X pairs and perturbs the transition to monoallelic Tsix expression required for Xist upregulation. While ablating DCP1A causes hyperpairing, forcing Tsix degradation resolves pairing and enables Xist upregulation. We link pairing to allelic partitioning of CCCTC-binding factor (CTCF) and show that tethering DCP1A to one Tsix allele is sufficient to drive monoallelic Xist expression. Thus, DCP1A flips a bistable switch for the mutually exclusive determination of active and inactive Xs.
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24
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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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25
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The Clinical Application of RNA Sequencing in Genetic Diagnosis of Mendelian Disorders. Clin Lab Med 2020; 40:121-133. [PMID: 32439064 DOI: 10.1016/j.cll.2020.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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da Silva Francisco Junior R, Dos Santos Ferreira C, Santos E Silva JC, Terra Machado D, Côrtes Martins Y, Ramos V, Simões Carnivali G, Garcia AB, Medina-Acosta E. Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins. Front Genet 2019; 10:1178. [PMID: 31850058 PMCID: PMC6887657 DOI: 10.3389/fgene.2019.01178] [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: 07/11/2019] [Accepted: 10/24/2019] [Indexed: 01/19/2023] Open
Abstract
Despite being developed from one zygote, heterokaryotypic monozygotic (MZ) co-twins exhibit discordant karyotypes. Epigenomic studies in biological samples from heterokaryotypic MZ co-twins are of the most significant value for assessing the effects on gene- and allele-specific expression of an extranumerary chromosomal copy or structural chromosomal disparities in otherwise nearly identical germline genetic contributions. Here, we use RNA-Seq data from existing repositories to establish within-pair correlations for the breadth and magnitude of allele-specific expression (ASE) in heterokaryotypic MZ co-twins discordant for trisomy 21 and maternal 21q inheritance, as well as homokaryotypic co-twins. We show that there is a genome-wide disparity at ASE sites between the heterokaryotypic MZ co-twins. Although most of the disparity corresponds to changes in the magnitude of biallelic imbalance, ASE sites switching from either strictly monoallelic to biallelic imbalance or the reverse occur in few genes that are known or predicted to be imprinted, subject to X-chromosome inactivation or A-to-I(G) RNA edited. We also uncovered comparable ASE differences between homokaryotypic MZ twins. The extent of ASE discordance in MZ twins (2.7%) was about 10-fold lower than the expected between pairs of unrelated, non-twin males or females. The results indicate that the observed within-pair dissimilarities in breadth and magnitude of ASE sites in the heterokaryotypic MZ co-twins could not solely be attributable to the aneuploidy and the missing allelic heritability at 21q.
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Affiliation(s)
| | - Cristina Dos Santos Ferreira
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Juan Carlo Santos E Silva
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Douglas Terra Machado
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Yasmmin Côrtes Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Victor Ramos
- Department of Genetics, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Gustavo Simões Carnivali
- Department of Computational Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Beatriz Garcia
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Enrique Medina-Acosta
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
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Bhagwan JR, Collins E, Mosqueira D, Bakar M, Johnson BB, Thompson A, Smith JG, Denning C. Variable expression and silencing of CRISPR-Cas9 targeted transgenes identifies the AAVS1 locus as not an entirely safe harbour. F1000Res 2019; 8:1911. [PMID: 32789000 PMCID: PMC7401084 DOI: 10.12688/f1000research.19894.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Diseases such as hypertrophic cardiomyopathy (HCM) can lead to severe outcomes including sudden death. The generation of human induced pluripotent stem cell (hiPSC) reporter lines can be useful for disease modelling and drug screening by providing physiologically relevant in vitro models of disease. The AAVS1 locus is cited as a safe harbour that is permissive for stable transgene expression, and hence is favoured for creating gene targeted reporter lines. Methods: We generated hiPSC reporters using a plasmid-based CRISPR/Cas9 nickase strategy. The first intron of PPP1R12C, the AAVS1 locus, was targeted with constructs expressing a genetically encoded calcium indicator (R-GECO1.0) or HOXA9-T2A-mScarlet reporter under the control of a pCAG or inducible pTRE promoter, respectively. Transgene expression was compared between clones before, during and/or after directed differentiation to mesodermal lineages. Results: Successful targeting to AAVS1 was confirmed by PCR and sequencing. Of 24 hiPSC clones targeted with pCAG-R-GECO1.0, only 20 expressed the transgene and in these, the percentage of positive cells ranged from 0% to 99.5%. Differentiation of a subset of clones produced cardiomyocytes, wherein the percentage of cells positive for R-GECO1.0 ranged from 2.1% to 93.1%. In the highest expressing R-GECO1.0 clones, transgene silencing occurred during cardiomyocyte differentiation causing a decrease in expression from 98.93% to 1.3%. In HOXA9-T2A-mScarlet hiPSC reporter lines directed towards mesoderm lineages, doxycycline induced a peak in transgene expression after two days but this reduced by up to ten-thousand-fold over the next 8-10 days. Nevertheless, for R-GECO1.0 lines differentiated into cardiomyocytes, transgene expression was rescued by continuous puromycin drug selection, which allowed the Ca 2+ responses associated with HCM to be investigated in vitro using single cell analysis. Conclusions: Targeted knock-ins to AAVS1 can be used to create reporter lines but variability between clones and transgene silencing requires careful attention by researchers seeking robust reporter gene expression.
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Affiliation(s)
- Jamie R. Bhagwan
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Emma Collins
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Diogo Mosqueira
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Mine Bakar
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Benjamin B. Johnson
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexander Thompson
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - James G.W. Smith
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Chris Denning
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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Bhagwan JR, Collins E, Mosqueira D, Bakar M, Johnson BB, Thompson A, Smith JG, Denning C. Variable expression and silencing of CRISPR-Cas9 targeted transgenes identifies the AAVS1 locus as not an entirely safe harbour. F1000Res 2019; 8:1911. [PMID: 32789000 PMCID: PMC7401084 DOI: 10.12688/f1000research.19894.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/22/2020] [Indexed: 01/11/2023] Open
Abstract
Background: Diseases such as hypertrophic cardiomyopathy (HCM) can lead to severe outcomes including sudden death. The generation of human induced pluripotent stem cell (hiPSC) reporter lines can be useful for disease modelling and drug screening by providing physiologically relevant in vitro models of disease. The AAVS1 locus is cited as a safe harbour that is permissive for stable transgene expression, and hence is favoured for creating gene targeted reporter lines. Methods: We generated hiPSC reporters using a plasmid-based CRISPR/Cas9 nickase strategy. The first intron of PPP1R12C, the AAVS1 locus, was targeted with constructs expressing a genetically encoded calcium indicator (R-GECO1.0) or HOXA9-T2A-mScarlet reporter under the control of a pCAG or inducible pTRE promoter, respectively. Transgene expression was compared between clones before, during and/or after directed differentiation to mesodermal lineages. Results: Successful targeting to AAVS1 was confirmed by PCR and sequencing. Of 24 hiPSC clones targeted with pCAG-R-GECO1.0, only 20 expressed the transgene and in these, the percentage of positive cells ranged from 0% to 99.5%. Differentiation of a subset of clones produced cardiomyocytes, wherein the percentage of cells positive for R-GECO1.0 ranged from 2.1% to 93.1%. In the highest expressing R-GECO1.0 clones, transgene silencing occurred during cardiomyocyte differentiation causing a decrease in expression from 98.93% to 1.3%. In HOXA9-T2A-mScarlet hiPSC reporter lines directed towards mesoderm lineages, doxycycline induced a peak in transgene expression after two days but this reduced by up to ten-thousand-fold over the next 8-10 days. Nevertheless, for R-GECO1.0 lines differentiated into cardiomyocytes, transgene expression was rescued by continuous puromycin drug selection, which allowed the Ca 2+ responses associated with HCM to be investigated in vitro using single cell analysis. Conclusions: Targeted knock-ins to AAVS1 can be used to create reporter lines but variability between clones and transgene silencing requires careful attention by researchers seeking robust reporter gene expression.
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Affiliation(s)
- Jamie R. Bhagwan
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Emma Collins
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Diogo Mosqueira
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Mine Bakar
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Benjamin B. Johnson
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexander Thompson
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - James G.W. Smith
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Chris Denning
- Department of Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
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29
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Wang H, Sawai A, Toji N, Sugioka R, Shibata Y, Suzuki Y, Ji Y, Hayase S, Akama S, Sese J, Wada K. Transcriptional regulatory divergence underpinning species-specific learned vocalization in songbirds. PLoS Biol 2019; 17:e3000476. [PMID: 31721761 PMCID: PMC6853299 DOI: 10.1371/journal.pbio.3000476] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 09/18/2019] [Indexed: 11/19/2022] Open
Abstract
Learning of most motor skills is constrained in a species-specific manner. However, the proximate mechanisms underlying species-specific learned behaviors remain poorly understood. Songbirds acquire species-specific songs through learning, which is hypothesized to depend on species-specific patterns of gene expression in functionally specialized brain regions for vocal learning and production, called song nuclei. Here, we leveraged two closely related songbird species, zebra finch, owl finch, and their interspecific first-generation (F1) hybrids, to relate transcriptional regulatory divergence between species with the production of species-specific songs. We quantified genome-wide gene expression in both species and compared this with allele-specific expression in F1 hybrids to identify genes whose expression in song nuclei is regulated by species divergence in either cis- or trans-regulation. We found that divergence in transcriptional regulation altered the expression of approximately 10% of total transcribed genes and was linked to differential gene expression between the two species. Furthermore, trans-regulatory changes were more prevalent than cis-regulatory and were associated with synaptic formation and transmission in song nucleus RA, the avian analog of the mammalian laryngeal motor cortex. We identified brain-derived neurotrophic factor (BDNF) as an upstream mediator of trans-regulated genes in RA, with a significant correlation between individual variation in BDNF expression level and species-specific song phenotypes in F1 hybrids. This was supported by the fact that the pharmacological overactivation of BDNF receptors altered the expression of its trans-regulated genes in the RA, thus disrupting the learned song structures of adult zebra finch songs at the acoustic and sequence levels. These results demonstrate functional neurogenetic associations between divergence in region-specific transcriptional regulation and species-specific learned behaviors.
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Affiliation(s)
- Hongdi Wang
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Azusa Sawai
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Noriyuki Toji
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Rintaro Sugioka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yukino Shibata
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yuika Suzuki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yu Ji
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shin Hayase
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Satoru Akama
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Jun Sese
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Humanome Lab Inc., Tokyo, Japan
| | - Kazuhiro Wada
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Faculty of Science, Hokkaido University, Sapporo, Japan
- Department of Biological Sciences, Hokkaido University, Sapporo, Japan
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30
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Benton MC, Lea RA, Macartney-Coxson D, Sutherland HG, White N, Kennedy D, Mengersen K, Haupt LM, Griffiths LR. Genome-wide allele-specific methylation is enriched at gene regulatory regions in a multi-generation pedigree from the Norfolk Island isolate. Epigenetics Chromatin 2019; 12:60. [PMID: 31594537 PMCID: PMC6781349 DOI: 10.1186/s13072-019-0304-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background Allele-specific methylation (ASM) occurs when DNA methylation patterns exhibit asymmetry among alleles. ASM occurs at imprinted loci, but its presence elsewhere across the human genome is indicative of wider importance in terms of gene regulation and disease risk. Here, we studied ASM by focusing on blood-based DNA collected from 24 subjects comprising a 3-generation pedigree from the Norfolk Island genetic isolate. We applied a genome-wide bisulphite sequencing approach with a genotype-independent ASM calling method to map ASM across the genome. Regions of ASM were then tested for enrichment at gene regulatory regions using Genomic Association Test (GAT) tool. Results In total, we identified 1.12 M CpGs of which 147,170 (13%) exhibited ASM (P ≤ 0.05). When including contiguous ASM signal spanning ≥ 2 CpGs, this condensed to 12,761 ASM regions (AMRs). These AMRs tagged 79% of known imprinting regions and most (98.1%) co-localised with known single nucleotide variants. Notably, miRNA and lncRNA showed a 3.3- and 1.8-fold enrichment of AMRs, respectively (P < 0.005). Also, the 5′ UTR and start codons each showed a 3.5-fold enrichment of AMRs (P < 0.005). There was also enrichment of AMRs observed at subtelomeric regions of many chromosomes. Five out of 11 large AMRs localised to the protocadherin cluster on chromosome 5. Conclusions This study shows ASM extends far beyond genomic imprinting in humans and that gene regulatory regions are hotspots for ASM. Future studies of ASM in pedigrees should help to clarify transgenerational inheritance patterns in relation to genotype and disease phenotypes.
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Affiliation(s)
- Miles C Benton
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Human Genomics, Institute of Environmental Science and Research, Wellington, New Zealand
| | - Rodney A Lea
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.
| | - Donia Macartney-Coxson
- Human Genomics, Institute of Environmental Science and Research, Wellington, New Zealand
| | - Heidi G Sutherland
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Nicole White
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Daniel Kennedy
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Kerry Mengersen
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
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31
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Zhang Y, Xue W, Zhang W, Yuan Y, Zhu X, Wang Q, Wei Y, Yang D, Yang C, Chen Y, Sun Y, Wang S, Huang K, Zheng L. Histone methyltransferase G9a protects against acute liver injury through GSTP1. Cell Death Differ 2019; 27:1243-1258. [PMID: 31515511 PMCID: PMC7206029 DOI: 10.1038/s41418-019-0412-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/01/2019] [Accepted: 08/16/2019] [Indexed: 11/24/2022] Open
Abstract
Acute liver injury is commonly caused by bacterial endotoxin/lipopolysaccharide (LPS), and by drug overdose such as acetaminophen (APAP). The exact role of epigenetic modification in acute liver injury remains elusive. Here, we investigated the role of histone methyltransferase G9a in LPS- or APAP overdose-induced acute liver injury. Under d-galactosamine sensitization, liver-specific G9a-deficient mice (L-G9a−/−) exhibited 100% mortality after LPS injection, while the control and L-G9a+/− littermates showed very mild mortality. Moreover, abrogation of hepatic G9a or inhibiting the methyltransferase activity of G9a aggravated LPS-induced liver damage. Similarly, under sublethal APAP overdose, L-G9a−/− mice displayed more severe liver injury. Mechanistically, ablation of G9a inhibited H3K9me1 levels at the promoters of Gstp1/2, two liver detoxifying enzymes, and consequently suppressed their transcription. Notably, treating L-G9a−/− mice with recombinant mouse GSTP1 reversed the LPS- or APAP overdose-induced liver damage. Taken together, we identify a novel beneficial role of G9a-GSTP1 axis in protecting against acute liver injury.
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Affiliation(s)
- Yu Zhang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, PR China
| | - Weili Xue
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, PR China
| | - Wenquan Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, PR China
| | - Yangmian Yuan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, PR China
| | - Xiuqin Zhu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, PR China
| | - Qing Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, PR China
| | - Yujuan Wei
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, PR China
| | - Dong Yang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, PR China
| | - Chen Yang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, PR China
| | - Yan Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, PR China
| | - Yu Sun
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, PR China
| | - Shun Wang
- Department of Blood Transfusion, Wuhan Hospital of Traditional and Western Medicine, Wuhan, 430022, PR China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, PR China.
| | - Ling Zheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, PR China.
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32
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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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33
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Yordanova I, Pavlova Z, Kirov A, Todorov T, Alexiev A, Sarafov S, Mateva L, Chamova T, Gospodinova M, Mitev V, Tournev I, Todorova A. Monoallelic expression of the TTR gene as a contributor to the age at onset and penetrance of TTR-related amyloidosis. Gene 2019; 705:16-21. [PMID: 30981840 DOI: 10.1016/j.gene.2019.04.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 11/18/2022]
Abstract
TTR-related amyloidosis (ATTR) is manifested in two allelic forms: familial amyloid polyneuropathy (TTR-FAP) and cardiomyopathy (TTR-FAC), both caused by mutations in the TTR gene. The most prevalent mutation in Bulgaria is p.Glu89Gln. Markedly different age at onset and disease penetrance is noticed in Bulgarian p.Glu89Gln cases even in a single family or between genetically identical twins. The present study aimed to evaluate the transcription profile of the TTR gene in order to better understand the difference in disease onset and penetrance. Six p.Glu89Gln positive families were selected from our registry, based on intrafamilial differences in disease onset and penetrance. Plasma and urine specimens were collected from 13 patients and subjected to transcription analysis. Both mutant and wild type transcripts were visualized in a mixed transcription profile, which is the traditional model of autosomal gene expression. The results from a relative quantification of the mutant versus wild type transcript showed presence of the mutant transcript between 0.14 and 1.14 times against the wild type. In addition, monoallelic expression signature was also detected. Based on our results we propose a model of natural selection, which includes age-related allele exclusion or suppression: predominant expression of a wild type (at an early age) and mutant (at the process of ageing) alleles. The intrafamilial differences in disease onset and penetrance need to be considered in genetic counselling and in follow-up of mutation carriers.
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Affiliation(s)
- Iglika Yordanova
- Genetic Medico-Diagnostic Laboratory Genica, Sofia, Bulgaria; IMDL Genome Center "Bulgaria", Sofia, Bulgaria
| | - Zornitza Pavlova
- IMDL Genome Center "Bulgaria", Sofia, Bulgaria; Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria
| | | | - Tihomir Todorov
- Genetic Medico-Diagnostic Laboratory Genica, Sofia, Bulgaria; IMDL Genome Center "Bulgaria", Sofia, Bulgaria
| | - Assen Alexiev
- Clinic of Gastroenterology, University Hospital "St. Ivan Rilski", Medical University-Sofia, Bulgaria
| | - Stayko Sarafov
- Clinic of Nervous Diseases, University Hospital "Alexandrovska", Department of Neurology, Medical University Sofia, Sofia, Bulgaria
| | - Lyudmila Mateva
- Clinic of Gastroenterology, University Hospital "St. Ivan Rilski", Medical University-Sofia, Bulgaria
| | - Teodora Chamova
- Clinic of Nervous Diseases, University Hospital "Alexandrovska", Department of Neurology, Medical University Sofia, Sofia, Bulgaria
| | | | - Vanyo Mitev
- Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria
| | - Ivailo Tournev
- Clinic of Nervous Diseases, University Hospital "Alexandrovska", Department of Neurology, Medical University Sofia, Sofia, Bulgaria; Department for Cognitive Science and Psychology, New Bulgarian University, Sofia, Bulgaria
| | - Albena Todorova
- Genetic Medico-Diagnostic Laboratory Genica, Sofia, Bulgaria; IMDL Genome Center "Bulgaria", Sofia, Bulgaria; Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria
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Wang Y, Gao S, Zhao Y, Chen WH, Shao JJ, Wang NN, Li M, Zhou GX, Wang L, Shen WJ, Xu JT, Deng WD, Wang W, Chen YL, Jiang Y. Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids. Zool Res 2019; 40:293-304. [PMID: 31271004 PMCID: PMC6680129 DOI: 10.24272/j.issn.2095-8137.2019.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Divergence of gene expression and alternative splicing is a crucial driving force in the evolution of species; to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expression (ASE) and allele-specific alternative splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interference of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horse×donkey (mule/hinny) and cattle×yak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, lncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptation. In conclusion, our study demonstrated that exploration of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Shan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Yue Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Wei-Huang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Jun-Jie Shao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Ni-Ni Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Guang-Xian Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Lei Wang
- Stake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining Qinghai 810016, China
| | - Wen-Jing Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Jing-Tao Xu
- Stake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining Qinghai 810016, China
| | - Wei-Dong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming Yunnan 650223, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Yu-Lin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China
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Abstract
BACKGROUND Monoallelic expression (MAE) is a frequent genomic phenomenon in normal tissues, however its role in cancer is yet to be fully understood. MAE is defined as the expression of a gene that is restricted to one allele in the presence of a diploid heterozygous genome. Constitutive MAE occurs for imprinted genes, odorant receptors and random X inactivation. Several studies in normal tissues have showed MAE in approximately 5-20% of the cases. However, little information exists on the MAE rate in cancer. In this study we assessed the presence and rate of MAE in melanoma. The genetic basis of melanoma has been studied in depth over the past decades, leading to the identification of mutations/genetic alterations responsible for melanoma development. METHODS To examine the role of MAE in melanoma we used 15 melanoma cell lines and compared their RNA-seq data with genotyping data obtained by the parental TIL (tumor infiltrating lymphocytes). Genotyping was performed using the Illumina HumanOmni1 beadchip. The RNA-seq library preparation and sequencing was performed using the Illumina TruSeq Stranded Total RNA Human Kit and subsequently sequenced using a HiSeq 2500 according to manufacturer's guidelines. By comparing genotyping data with RNA-seq data, we identified SNPs in which DNA genotypes were heterozygous and corresponding RNA genotypes were homozygous. All homozygous DNA genotypes were removed prior to the analysis. To confirm the validity to detect MAE, we examined heterozygous DNA genotypes from X chromosome of female samples as well as for imprinted and olfactory receptor genes and confirmed MAE. RESULTS MAE was detected in all 15 cell lines although to a different rate. When looking at the B-allele frequencies we found a preferential pattern of complete monoallelic expression rather then differential monoallelic expression across the 15 melanoma cell lines. As some samples showed high differences in the homozygous and heterozygous call rate, we looked at the single chromosomes and showed that MAE may be explained by underlying large copy number imbalances in some instances. Interestingly these regions included genes known to play a role in melanoma initiation and progression. Nevertheless, some chromosome regions showed MAE without CN imbalances suggesting that additional mechanisms (including epigenetic silencing) may explain MAE in melanoma. CONCLUSION The biological implications of MAE are yet to be realized. Nevertheless, our findings suggest that MAE is a common phenomenon in melanoma cell lines. Further analyses are currently being undertaken to evaluate whether MAE is gene/pathway specific and to understand whether MAE can be employed by cancers to achieve a more aggressive phenotype.
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Matos I, Machado MP, Schartl M, Coelho MM. Allele-specific expression variation at different ploidy levels in Squalius alburnoides. Sci Rep 2019; 9:3688. [PMID: 30842567 PMCID: PMC6403402 DOI: 10.1038/s41598-019-40210-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/07/2019] [Indexed: 11/09/2022] Open
Abstract
Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides. Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides.
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Affiliation(s)
- Isa Matos
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal.,University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany
| | - Miguel P Machado
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal.,University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany.,Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Manfred Schartl
- University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany. .,Comprehensive Cancer Center, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA.
| | - Maria Manuela Coelho
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal
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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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38
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Abstract
Malignant blood disorders depend on heritable susceptibility genes and occur in familial aggregations. We suggest a model of transgenerational segregation of the susceptibility genes based on the study of malignant blood disorders in Norwegian and Danish families with unrelated parents, and in the inbred Faroese population with related parents. This model, consisting of parental genomic imprinting and mother-son microchimerism, can explain the male predominance in most of the diseases, the predominance of affected parent-offspring when parents are not related, and the different modes of segregation in males and females. The model displays a specific pattern in the distribution of affected relatives for each diagnosis, viz. a characteristic distribution in the pedigrees of family members with malignant blood disorder related to the proband. Three such patterns, each reflecting a specific transgenerational passage, were identified: (1) alterations in the number of affected relatives in paternal lines alone, e.g. in patterns for probands with multiple myeloma; (2) alterations in the number of affected relatives in both paternal and maternal lines for probands with chronic lymphocytic leukemia; and (3) no alterations in the numbers of male and female affected relatives in the parental lines, e.g. for probands with some types of malignant lymphoma.
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39
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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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40
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Smith JGW, Owen T, Bhagwan JR, Mosqueira D, Scott E, Mannhardt I, Patel A, Barriales-Villa R, Monserrat L, Hansen A, Eschenhagen T, Harding SE, Marston S, Denning C. Isogenic Pairs of hiPSC-CMs with Hypertrophic Cardiomyopathy/LVNC-Associated ACTC1 E99K Mutation Unveil Differential Functional Deficits. Stem Cell Reports 2018; 11:1226-1243. [PMID: 30392975 PMCID: PMC6235010 DOI: 10.1016/j.stemcr.2018.10.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a primary disorder of contractility in heart muscle. To gain mechanistic insight and guide pharmacological rescue, this study models HCM using isogenic pairs of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) carrying the E99K-ACTC1 cardiac actin mutation. In both 3D engineered heart tissues and 2D monolayers, arrhythmogenesis was evident in all E99K-ACTC1 hiPSC-CMs. Aberrant phenotypes were most common in hiPSC-CMs produced from the heterozygote father. Unexpectedly, pathological phenotypes were less evident in E99K-expressing hiPSC-CMs from the two sons. Mechanistic insight from Ca2+ handling expression studies prompted pharmacological rescue experiments, wherein dual dantroline/ranolazine treatment was most effective. Our data are consistent with E99K mutant protein being a central cause of HCM but the three-way interaction between the primary genetic lesion, background (epi)genetics, and donor patient age may influence the pathogenic phenotype. This illustrates the value of isogenic hiPSC-CMs in genotype-phenotype correlations.
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Affiliation(s)
- James G W Smith
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK; Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7UQ, UK.
| | - Thomas Owen
- National Heart and Lung Institute, Imperial College, London W12 0NN, UK
| | - Jamie R Bhagwan
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Diogo Mosqueira
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Elizabeth Scott
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Ingra Mannhardt
- Institute of Experimental Pharmacology and Toxicology, University Medical Centre, Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Asha Patel
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK; Department of Gene Therapy, National Heart and Lung Institute, Imperial College London SW3 6LR, UK
| | - Roberto Barriales-Villa
- Inherited Cardiovascular Diseases Unit, Cardiology Service, Complexo Hospitalario Universitario A Coruña, Servizo Galego de Saúde (SERGAS), Universidade da Coruña, A Coruña, Spain; Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
| | - Lorenzo Monserrat
- Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain; Health in Code S.L., Cardiology Department, A Coruña, Spain
| | - Arne Hansen
- Institute of Experimental Pharmacology and Toxicology, University Medical Centre, Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Thomas Eschenhagen
- Institute of Experimental Pharmacology and Toxicology, University Medical Centre, Hamburg-Eppendorf, Hamburg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Sian E Harding
- National Heart and Lung Institute, Imperial College, London W12 0NN, UK
| | - Steve Marston
- National Heart and Lung Institute, Imperial College, London W12 0NN, UK
| | - Chris Denning
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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41
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Stenton SL, Prokisch H. The Clinical Application of RNA Sequencing in Genetic Diagnosis of Mendelian Disorders. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.yamp.2018.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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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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43
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Khamlichi AA, Feil R. Parallels between Mammalian Mechanisms of Monoallelic Gene Expression. Trends Genet 2018; 34:954-971. [PMID: 30217559 DOI: 10.1016/j.tig.2018.08.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/06/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
Different types of monoallelic gene expression are present in mammals, some of which are highly flexible, whereas others are more rigid. These include allelic exclusion at antigen receptor loci, the expression of olfactory receptor genes, genomic imprinting, X-chromosome inactivation, and random monoallelic expression (MAE). Although these processes play diverse biological roles, and arose through different selective pressures, the underlying epigenetic mechanisms show striking resemblances. Regulatory transcriptional events are important in all systems, particularly in the specification of MAE. Combined with comparative studies between species, this suggests that the different MAE systems found in mammals may have evolved from analogous ancestral processes.
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Affiliation(s)
- Ahmed Amine Khamlichi
- Institute of Pharmacology and Structural Biology (IPBS), Centre National de la Recherche Scientifique (CNRS) and Paul Sabatier University (UPS), 205 route de Narbonne, 31077 Toulouse, France.
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and the University of Montpellier, 1919 route de Mende, 34293 Montpellier, France.
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SanMiguel JM, Abramowitz LK, Bartolomei MS. Imprinted gene dysregulation in a Tet1 null mouse model is stochastic and variable in the germline and offspring. Development 2018; 145:dev.160622. [PMID: 29530881 PMCID: PMC5963867 DOI: 10.1242/dev.160622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/04/2018] [Indexed: 12/15/2022]
Abstract
Imprinted genes are expressed from one parental allele and regulated by differential DNA methylation at imprinting control regions (ICRs). ICRs are reprogrammed in the germline through erasure and re-establishment of DNA methylation. Although much is known about DNA methylation establishment, DNA demethylation is less well understood. Recently, the Ten-Eleven Translocation proteins (TET1-3) have been shown to initiate DNA demethylation, with Tet1-/- mice exhibiting aberrant levels of imprinted gene expression and ICR methylation. Nevertheless, the role of TET1 in demethylating ICRs in the female germline and in controlling allele-specific expression remains unknown. Here, we examined ICR-specific DNA methylation in Tet1-/- germ cells and ascertained whether abnormal ICR methylation impacted imprinted gene expression in F1 hybrid somatic tissues derived from Tet1-/- eggs or sperm. We show that Tet1 deficiency is associated with hypermethylation of a subset of ICRs in germ cells. Moreover, ICRs with defective germline reprogramming exhibit aberrant DNA methylation and biallelic expression of linked imprinted genes in somatic tissues. Thus, we define a discrete set of genomic regions that require TET1 for germline reprogramming and discuss mechanisms for stochastic imprinting defects.
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Affiliation(s)
- Jennifer M SanMiguel
- University of Pennsylvania, Perelman School of Medicine, Department of Cell and Developmental Biology, SCTR 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Lara K Abramowitz
- University of Pennsylvania, Perelman School of Medicine, Department of Cell and Developmental Biology, SCTR 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.,Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marisa S Bartolomei
- University of Pennsylvania, Perelman School of Medicine, Department of Cell and Developmental Biology, SCTR 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
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45
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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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46
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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: 8] [Impact Index Per Article: 1.1] [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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47
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Han Y, Chu X, Yu H, Ma YK, Wang XJ, Qian W, Jiao Y. Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells. Sci Bull (Beijing) 2017; 62:1304-1314. [PMID: 36659292 DOI: 10.1016/j.scib.2017.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 01/21/2023]
Abstract
Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica (93-11) and japonica (Nipponbare) inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By contrast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of-origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9ac/H3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.
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Affiliation(s)
- Yingying Han
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haopeng Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Ke Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiu-Jie Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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48
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Al-Tobasei R, Ali A, Leeds TD, Liu S, Palti Y, Kenney B, Salem M. Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout. BMC Genomics 2017; 18:582. [PMID: 28784089 PMCID: PMC5547479 DOI: 10.1186/s12864-017-3992-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 08/01/2017] [Indexed: 12/22/2022] Open
Abstract
Background Coding/functional SNPs change the biological function of a gene and, therefore, could serve as “large-effect” genetic markers. In this study, we used two bioinformatics pipelines, GATK and SAMtools, for discovering coding/functional SNPs with allelic-imbalances associated with total body weight, muscle yield, muscle fat content, shear force, and whiteness. Phenotypic data were collected for approximately 500 fish, representing 98 families (5 fish/family), from a growth-selected line, and the muscle transcriptome was sequenced from 22 families with divergent phenotypes (4 low- versus 4 high-ranked families per trait). Results GATK detected 59,112 putative SNPs; of these SNPs, 4798 showed allelic imbalances (>2.0 as an amplification and <0.5 as loss of heterozygosity). SAMtools detected 87,066 putative SNPs; and of them, 4962 had allelic imbalances between the low- and high-ranked families. Only 1829 SNPs with allelic imbalances were common between the two datasets, indicating significant differences in algorithms. The two datasets contained 7930 non-redundant SNPs of which 4439 mapped to 1498 protein-coding genes (with 6.4% non-synonymous SNPs) and 684 mapped to 295 lncRNAs. Validation of a subset of 92 SNPs revealed 1) 86.7–93.8% success rate in calling polymorphic SNPs and 2) 95.4% consistent matching between DNA and cDNA genotypes indicating a high rate of identifying SNPs with allelic imbalances. In addition, 4.64% SNPs revealed random monoallelic expression. Genome distribution of the SNPs with allelic imbalances exhibited high density for all five traits in several chromosomes, especially chromosome 9, 20 and 28. Most of the SNP-harboring genes were assigned to important growth-related metabolic pathways. Conclusion These results demonstrate utility of RNA-Seq in assessing phenotype-associated allelic imbalances in pooled RNA-Seq samples. The SNPs identified in this study were included in a new SNP-Chip design (available from Affymetrix) for genomic and genetic analyses in rainbow trout. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3992-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Ali Ali
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Timothy D Leeds
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, 25430, USA
| | - Sixin Liu
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, 25430, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, 25430, USA
| | - Brett Kenney
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Mohamed Salem
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA. .,Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
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49
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Kremer LS, Bader DM, Mertes C, Kopajtich R, Pichler G, Iuso A, Haack TB, Graf E, Schwarzmayr T, Terrile C, Koňaříková E, Repp B, Kastenmüller G, Adamski J, Lichtner P, Leonhardt C, Funalot B, Donati A, Tiranti V, Lombes A, Jardel C, Gläser D, Taylor RW, Ghezzi D, Mayr JA, Rötig A, Freisinger P, Distelmaier F, Strom TM, Meitinger T, Gagneur J, Prokisch H. Genetic diagnosis of Mendelian disorders via RNA sequencing. Nat Commun 2017; 8:15824. [PMID: 28604674 PMCID: PMC5499207 DOI: 10.1038/ncomms15824] [Citation(s) in RCA: 355] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/28/2017] [Indexed: 12/23/2022] Open
Abstract
Across a variety of Mendelian disorders, ∼50-75% of patients do not receive a genetic diagnosis by exome sequencing indicating disease-causing variants in non-coding regions. Although genome sequencing in principle reveals all genetic variants, their sizeable number and poorer annotation make prioritization challenging. Here, we demonstrate the power of transcriptome sequencing to molecularly diagnose 10% (5 of 48) of mitochondriopathy patients and identify candidate genes for the remainder. We find a median of one aberrantly expressed gene, five aberrant splicing events and six mono-allelically expressed rare variants in patient-derived fibroblasts and establish disease-causing roles for each kind. Private exons often arise from cryptic splice sites providing an important clue for variant prioritization. One such event is found in the complex I assembly factor TIMMDC1 establishing a novel disease-associated gene. In conclusion, our study expands the diagnostic tools for detecting non-exonic variants and provides examples of intronic loss-of-function variants with pathological relevance.
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Affiliation(s)
- Laura S. Kremer
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Daniel M. Bader
- Department of Informatics, Technische Universität München, 85748 Garching, Germany
- Quantitative Biosciences Munich, Gene Center, Department of Biochemistry, Ludwig Maximilian Universität München, 81377 München, Germany
| | - Christian Mertes
- Department of Informatics, Technische Universität München, 85748 Garching, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Garwin Pichler
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Arcangela Iuso
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Tobias B. Haack
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Caterina Terrile
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Eliška Koňaříková
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Birgit Repp
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | | | - Benoit Funalot
- INSERM U1163, Université Paris Descartes—Sorbonne Paris Cité, Institut Imagine, 75015 Paris, France
| | - Alice Donati
- Metabolic Unit, A. Meyer Children’s Hospital, 50139 Florence, Italy
| | - Valeria Tiranti
- Unit of Molecular Neurogenetics, Foundation IRCCS (Istituto di Ricovero e Cura a Carettere Scientifico) Neurological Institute ‘Carlo Besta’, 20126 Milan, Italy
| | - Anne Lombes
- Inserm UMR 1016, Institut Cochin, 75014 Paris, France
- CNRS UMR 8104, Institut Cochin, 75014 Paris, France
- Université Paris V René Descartes, Institut Cochin, 75014 Paris, France
| | - Claude Jardel
- Inserm UMR 1016, Institut Cochin, 75014 Paris, France
- AP/HP, GHU Pitié-Salpêtrière, Service de Biochimie Métabolique, 75013 Paris, France
| | - Dieter Gläser
- Genetikum, Genetic Counseling and Diagnostics, 89231 Neu-Ulm, Germany
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Daniele Ghezzi
- Unit of Molecular Neurogenetics, Foundation IRCCS (Istituto di Ricovero e Cura a Carettere Scientifico) Neurological Institute ‘Carlo Besta’, 20126 Milan, Italy
| | - Johannes A. Mayr
- Department of Pediatrics, Paracelsus Medical University, A-5020 Salzburg, Austria
| | - Agnes Rötig
- INSERM U1163, Université Paris Descartes—Sorbonne Paris Cité, Institut Imagine, 75015 Paris, France
| | - Peter Freisinger
- Department of Pediatrics, Klinikum Reutlingen, 72764 Reutlingen, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children’s Hospital, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Tim M. Strom
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
| | - Julien Gagneur
- Department of Informatics, Technische Universität München, 85748 Garching, Germany
- Quantitative Biosciences Munich, Gene Center, Department of Biochemistry, Ludwig Maximilian Universität München, 81377 München, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, 81675 München, Germany
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50
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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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