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Zou LS, Cable DM, Barrera-Lopez IA, Zhao T, Murray E, Aryee MJ, Chen F, Irizarry RA. Detection of allele-specific expression in spatial transcriptomics with spASE. Genome Biol 2024; 25:180. [PMID: 38978101 PMCID: PMC11229351 DOI: 10.1186/s13059-024-03317-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framework for detecting and estimating spatial ASE. To tackle the challenges presented by cell type mixtures and a low signal to noise ratio, we implement a hierarchical model involving additive mixtures of spatial smoothing splines. We apply our method to allele-resolved Visium and Slide-seq from the mouse cerebellum and hippocampus and report new insight into the landscape of spatial and cell type-specific ASE therein.
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Affiliation(s)
- Luli S Zou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Dylan M Cable
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, 02139, USA
| | | | - Tongtong Zhao
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Martin J Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Rafael A Irizarry
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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2
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Kanata E, Duffié R, Schulz EG. Establishment and maintenance of random monoallelic expression. Development 2024; 151:dev201741. [PMID: 38813842 PMCID: PMC11166465 DOI: 10.1242/dev.201741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
This Review elucidates the regulatory principles of random monoallelic expression by focusing on two well-studied examples: the X-chromosome inactivation regulator Xist and the olfactory receptor gene family. Although the choice of a single X chromosome or olfactory receptor occurs in different developmental contexts, common gene regulatory principles guide monoallelic expression in both systems. In both cases, an event breaks the symmetry between genetically and epigenetically identical copies of the gene, leading to the expression of one single random allele, stabilized through negative feedback control. Although many regulatory steps that govern the establishment and maintenance of monoallelic expression have been identified, key pieces of the puzzle are still missing. We provide an overview of the current knowledge and models for the monoallelic expression of Xist and olfactory receptors. We discuss their similarities and differences, and highlight open questions and approaches that could guide the study of other monoallelically expressed genes.
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Affiliation(s)
- Eleni Kanata
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Rachel Duffié
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Edda G. Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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3
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Kapural L, Mekhail NA, Costandi S, Gilmore C, Pope JE, Li S, Hunter CW, Poree L, Staats PS, Taylor RS, Eldabe S, Kallewaard JW, Thomson S, Petersen EA, Sayed D, Deer TR, Antony A, Budwany R, Leitner A, Soliday N, Duarte RV, Levy RM. Durable multimodal and holistic response for physiologic closed-loop spinal cord stimulation supported by objective evidence from the EVOKE double-blind randomized controlled trial. Reg Anesth Pain Med 2024; 49:233-240. [PMID: 37491149 DOI: 10.1136/rapm-2023-104639] [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: 04/29/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023]
Abstract
INTRODUCTION Chronic pain patients may experience impairments in multiple health-related domains. The design and interpretation of clinical trials of chronic pain interventions, however, remains primarily focused on treatment effects on pain intensity. This study investigates a novel, multidimensional holistic treatment response to evoked compound action potential-controlled closed-loop versus open-loop spinal cord stimulation as well as the degree of neural activation that produced that treatment response. METHODS Outcome data for pain intensity, physical function, health-related quality of life, sleep quality and emotional function were derived from individual patient level data from the EVOKE multicenter, participant, investigator, and outcome assessor-blinded, parallel-arm randomized controlled trial with 24 month follow-up. Evaluation of holistic treatment response considered whether the baseline score was worse than normative values and whether minimal clinical important differences were reached in each of the domains that were impaired at baseline. A cumulative responder score was calculated to reflect the total minimal clinical important differences accumulated across all domains. Objective neurophysiological data, including spinal cord activation were measured. RESULTS Patients were randomized to closed-loop (n=67) or open-loop (n=67). A greater proportion of patients with closed-loop spinal cord stimulation (49.3% vs 26.9%) were holistic responders at 24-month follow-up, with at least one minimal clinical important difference in all impaired domains (absolute risk difference: 22.4%, 95% CI 6.4% to 38.4%, p=0.012). The cumulative responder score was significantly greater for closed-loop patients at all time points and resulted in the achievement of more than three additional minimal clinical important differences at 24-month follow-up (mean difference 3.4, 95% CI 1.3 to 5.5, p=0.002). Neural activation was three times more accurate in closed-loop spinal cord stimulation (p<0.001 at all time points). CONCLUSION The results of this study suggest that closed-loop spinal cord stimulation can provide sustained clinically meaningful improvements in multiple domains and provide holistic improvement in the long-term for patients with chronic refractory pain. TRIAL REGISTRATION NUMBER NCT02924129.
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Affiliation(s)
- Leonardo Kapural
- Carolinas Pain Institute, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | | | | | | | - Jason E Pope
- Evolve Restorative Center, Santa Rosa, California, USA
| | - Sean Li
- Premier Pain Centers, Shrewsbury, New Jersey, USA
| | - Corey W Hunter
- Ainsworth Institute of Pain Management, New York, New York, USA
| | - Lawrence Poree
- University of California at San Francisco, San Francisco, California, USA
| | | | - Rod S Taylor
- Institute of Health and Well Being, University of Glasgow, Glasgow, UK
| | - Sam Eldabe
- Pain Medicine, James Cook Univesity Hospital, Middlesbrough, UK
| | - Jan Willem Kallewaard
- Anesthesiology and Pain Medicine, Rijnstate Hospital, Arnhem, The Netherlands
- Anesthesiology and Pain Medicine, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Simon Thomson
- Pain Medicine and Neuromodulation, Mid & South Essex University Hospitals, Essex, UK
| | - Erika A Petersen
- University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Dawood Sayed
- The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Timothy R Deer
- Spine and Nerve Center of the Virginias, West Virginia University - Health Sciences Campus, Morgantown, West Virginia, USA
| | - Ajay Antony
- The Orthopaedic Institute, Gainesville, Florida, USA
| | - Ryan Budwany
- West Virginia University, Morgantown, West Virginia, USA
| | - Angela Leitner
- Saluda Medical Pty Ltd, Artarmon, New South Wales, Australia
| | - Nicole Soliday
- Saluda Medical Pty Ltd, Artarmon, New South Wales, Australia
| | - Rui V Duarte
- Saluda Medical Pty Ltd, Artarmon, New South Wales, Australia
- Health Data Science, University of Liverpool, Liverpool, UK
| | - Robert M Levy
- Anesthesia Pain Care Consultants, Boca Raton, Florida, USA
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4
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Jiang J, Tan S, Feng X, Peng Y, Long C, Yang L. Distinct ACC Neural Mechanisms Underlie Authentic and Transmitted Anxiety Induced by Maternal Separation in Mice. J Neurosci 2023; 43:8201-8218. [PMID: 37845036 PMCID: PMC10697407 DOI: 10.1523/jneurosci.0558-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 10/18/2023] Open
Abstract
It is known that humans and rodents are capable of transmitting stress to their naive partners via social interaction. However, a comprehensive understanding of transmitted stress, which may differ from authentic stress, thus revealing unique neural mechanisms of social interaction resulting from transmitted stress and the associated anxiety, is missing. We used, in the present study, maternal separation (MS) as a stress model to investigate whether MS causes abnormal behavior in adolescence. A key concern in the analysis of stress transmission is whether the littermates of MS mice who only witness MS stress ("Partners") exhibit behavioral abnormalities similar to those of MS mice themselves. Of special interest is the establishment of the neural mechanisms underlying transmitted stress and authentic stress. The results show that Partners, similar to MS mice, exhibit anxiety-like behavior and hyperalgesia after witnessing littermates being subjected to early-life repetitive MS. Electrophysiological analysis revealed that mice subjected to MS demonstrate a reduction in both the excitatory and inhibitory synaptic activities of parvalbumin interneurons (PVINs) in the anterior cingulate cortex (ACC). However, Partners differed from MS mice in showing an increase in the number and excitability of GABAergic PVINs in the ACC and in the ability of chemogenetic PVIN inactivation to eliminate abnormal behavior. Furthermore, the social transfer of anxiety-like behavior required intact olfactory, but not visual, perception. This study suggests a functional involvement of ACC PVINs in mediating the distinct neural basis of transmitted anxiety.SIGNIFICANCE STATEMENT The anterior cingulate cortex (ACC) is a critical brain area in physical and social pain and contributes to the exhibition of abnormal behavior. ACC glutamatergic neurons have been shown to encode transmitted stress, but it remains unclear whether inhibitory ACC neurons also play a role. We evaluate, in this study, ACC neuronal, synaptic and network activities and uncover a critical role of parvalbumin interneurons (PVINs) in the expression of transmitted stress in adolescent mice who had witnessed MS of littermates in infancy. Furthermore, inactivation of ACC PVINs blocks transmitted stress. The results suggest that emotional contagion has a severe effect on brain function, and identify a potential target for the treatment of transmitted anxiety.
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Affiliation(s)
- Jinxiang Jiang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shuyi Tan
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaoyi Feng
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yigang Peng
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Cheng Long
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Li Yang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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5
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He Z, Li S, Mo L, Zheng Z, Li Y, Li H, Zhang D. The VLPFC-Engaged Voluntary Emotion Regulation: Combined TMS-fMRI Evidence for the Neural Circuit of Cognitive Reappraisal. J Neurosci 2023; 43:6046-6060. [PMID: 37507228 PMCID: PMC10451149 DOI: 10.1523/jneurosci.1337-22.2023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023] Open
Abstract
A clear understanding of the neural circuit underlying emotion regulation (ER) is important for both basic and translational research. However, a lack of evidence based on combined neuroimaging and neuromodulation techniques calls into question (1) whether the change of prefrontal-subcortical activity intrinsically and causally contributes to the ER effect; and (2) whether the prefrontal control system directly modulates the subcortical affective system. Accordingly, we combined fMRI recordings with transcranial magnetic stimulation (TMS) to map the causal connections between the PFC and subcortical affective structures (amygdala and insula). A total of 117 human adult participants (57 males and 60 females) were included in the study. The results revealed that TMS-induced ventrolateral PFC (VLPFC) facilitation led to enhanced activity in the VLPFC and ventromedial PFC (VMPFC) as well as attenuated activity in the amygdala and insula during reappraisal but not during nonreappraisal (i.e., baseline). Moreover, the activated VLPFC intensified the prefrontal-subcortical couplings via the VMPFC during reappraisal only. This study provides combined TMS-fMRI evidence that downregulating negative emotion involves the prefrontal control system suppressing the subcortical affective system, with the VMPFC serving as a crucial hub within the VLPFC-subcortical network, suggesting an indirect pathway model of the ER circuit. Our findings outline potential protocols for improving ER ability by intensifying the VLPFC-VMPFC coupling in patients with mood and anxiety disorders.SIGNIFICANCE STATEMENT Using fMRI to examine the TMS effect, we uncovered that the opposite neural changes in prefrontal (enhanced) and subcortical (attenuated) regions are not a byproduct of emotion regulation (ER); instead, this prefrontal-subcortical activity per se causally contributes to the ER effect. Furthermore, using TMS to amplify the neural changes within the ER circuit, the "bridge" role of the VMPFC is highlighted under the reappraisal versus nonreappraisal contrast. This "perturb-and-measure" approach overcomes the correlational nature of fMRI data, helping us to identify brain regions that causally support reappraisal (the VLPFC and VMPFC) and those that are modulated by reappraisal (the amygdala and insula). The uncovered ER circuit is important for understanding the neural systems underlying reappraisal and valuable for translational research.
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Affiliation(s)
- Zhenhong He
- Institute of Brain and Psychological Sciences, Sichuan Normal University, Chengdu, 610066, China
- School of Psychology, Shenzhen University, Shenzhen, 518060, China
| | - Sijin Li
- School of Psychology, Shenzhen University, Shenzhen, 518060, China
| | - Licheng Mo
- School of Psychology, Shenzhen University, Shenzhen, 518060, China
| | - Zixin Zheng
- Institute of Brain and Psychological Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Yiwei Li
- Institute of Brain and Psychological Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Hong Li
- Institute of Brain and Psychological Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Dandan Zhang
- Institute of Brain and Psychological Sciences, Sichuan Normal University, Chengdu, 610066, China
- Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, 518055, China
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Heskett MB, Vouzas AE, Smith LG, Yates PA, Boniface C, Bouhassira EE, Spellman PT, Gilbert DM, Thayer MJ. Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability. Nat Commun 2022; 13:6301. [PMID: 36273230 PMCID: PMC9588035 DOI: 10.1038/s41467-022-34099-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/13/2022] [Indexed: 01/18/2023] Open
Abstract
ASARs are long noncoding RNA genes that control replication timing of entire human chromosomes in cis. The three known ASAR genes are located on human chromosomes 6 and 15, and are essential for chromosome integrity. To identify ASARs on all human chromosomes we utilize a set of distinctive ASAR characteristics that allow for the identification of hundreds of autosomal loci with epigenetically controlled, allele-restricted behavior in expression and replication timing of coding and noncoding genes, and is distinct from genomic imprinting. Disruption of noncoding RNA genes at five of five tested loci result in chromosome-wide delayed replication and chromosomal instability, validating their ASAR activity. In addition to the three known essential cis-acting chromosomal loci, origins, centromeres, and telomeres, we propose that all mammalian chromosomes also contain "Inactivation/Stability Centers" that display allele-restricted epigenetic regulation of protein coding and noncoding ASAR genes that are essential for replication and stability of each chromosome.
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Affiliation(s)
- Michael B Heskett
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Molecular and Medical Genetics Oregon Health & Science University, Portland, OR, 97239, USA
| | - Athanasios E Vouzas
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Leslie G Smith
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA
| | - Phillip A Yates
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA
| | - Christopher Boniface
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eric E Bouhassira
- Department of Cell Biology and Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Paul T Spellman
- Department of Molecular and Medical Genetics Oregon Health & Science University, Portland, OR, 97239, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute Oregon Health & Science University, Portland, OR, 97239, USA
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Mathew J Thayer
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA.
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7
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Chen SY, Li C, Luo Z, Li X, Jia X, Lai SJ. Favoring Expression of Yak Alleles in Interspecies F1 Hybrids of Cattle and Yak Under High-Altitude Environments. Front Vet Sci 2022; 9:892663. [PMID: 35847643 PMCID: PMC9280030 DOI: 10.3389/fvets.2022.892663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/01/2022] [Indexed: 11/29/2022] Open
Abstract
Both cis- and trans-regulation could cause differential expression between the parental alleles in diploid species that might have broad biological implications. Due to the relatively distant genetic divergence between cattle and yak, as well as their differential adaptation to high-altitude environments, we investigated genome-wide allelic differential expression (ADE) in their F1 hybrids using Nanopore long-read RNA-seq technology. From adult F1 hybrids raised in high-altitude, ten lung and liver tissues were individually sequenced for producing 31.6 M full-length transcript sequences. Mapping against autosomal homologous regions between cattle and yak, we detected 17,744 and 14,542 protein-encoding genes expressed in lung and liver tissues, respectively. According to the parental assignments of transcript sequences, a total of 3,381 genes were detected to show ADE in at least one sample. There were 186 genes showing ubiquitous ADE in all the studied animals, and among them 135 and 37 genes had consistent higher expression of yak and cattle alleles, respectively. Functional analyses revealed that the genes with favoring expression of yak alleles have been involved in the biological progresses related with hypoxia adaptation and immune response. In contrast, the genes with favoring expression of cattle alleles have been enriched into different biological progresses, such as secretion of endocrine hormones and lipid metabolism. Our results would support unequal contribution of parental genes to environmental adaptation in the F1 hybrids of cattle and yak.
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Affiliation(s)
- Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Shi-Yi Chen
| | - Cao Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhihao Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Longri Breeding Farm of Sichuan Province, Hongyuan, China
| | - Xiaowei Li
- Longri Breeding Farm of Sichuan Province, Hongyuan, China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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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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9
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Sen A, Huo Y, Elster J, Zage PE, McVicker G. Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma. Genome Biol 2022; 23:71. [PMID: 35246212 PMCID: PMC8896304 DOI: 10.1186/s13059-022-02640-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neuroblastoma is a pediatric malignancy with a high frequency of metastatic disease at initial diagnosis. Neuroblastoma tumors have few recurrent protein-coding mutations but contain extensive somatic copy number alterations (SCNAs) suggesting that mutations that alter gene dosage are important drivers of tumorigenesis. Here, we analyze allele-specific expression in 96 high-risk neuroblastoma tumors to discover genes impacted by cis-acting mutations that alter dosage. RESULTS We identify 1043 genes with recurrent, neuroblastoma-specific allele-specific expression. While most of these genes lie within common SCNA regions, many of them exhibit allele-specific expression in copy neutral samples and these samples are enriched for mutations that are predicted to cause nonsense-mediated decay. Thus, both SCNA and non-SCNA mutations frequently alter gene expression in neuroblastoma. We focus on genes with neuroblastoma-specific allele-specific expression in the absence of SCNAs and find 26 such genes that have reduced expression in stage 4 disease. At least two of these genes have evidence for tumor suppressor activity including the transcription factor TFAP2B and the protein tyrosine phosphatase PTPRH. CONCLUSIONS In summary, our allele-specific expression analysis discovers genes that are recurrently dysregulated by both large SCNAs and other cis-acting mutations in high-risk neuroblastoma.
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Affiliation(s)
- Arko Sen
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Yuchen Huo
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego, La Jolla, California, USA
| | - Jennifer Elster
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego, La Jolla, California, USA.,Peckham Center for Cancer and Blood Disorders, Rady Children's Hospital-San Diego, San Diego, California, USA
| | - Peter E Zage
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego, La Jolla, California, USA.,Peckham Center for Cancer and Blood Disorders, Rady Children's Hospital-San Diego, San Diego, California, USA
| | - Graham McVicker
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA.
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10
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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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11
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Chromosomal coordination and differential structure of asynchronous replicating regions. Nat Commun 2021; 12:1035. [PMID: 33589603 PMCID: PMC7884787 DOI: 10.1038/s41467-021-21348-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/18/2021] [Indexed: 02/05/2023] Open
Abstract
Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells. By taking advantage of stable clonal pre-B cell populations derived from C57BL6/Castaneous mice, we have mapped the genome-wide AS-RT loci, independently of genetic differences. These regions are characterized by differential chromatin accessibility, mono-allelic expression and include new gene families involved in specifying cell identity. By combining population level mapping with single cell FISH, our data reveal the existence of a novel regulatory program that coordinates a fixed relationship between AS-RT regions on any given chromosome, with some loci set to replicate in a parallel and others set in the anti-parallel orientation. Our results show that AS-RT is a highly regulated epigenetic mark established during early embryogenesis that may be used for facilitating the programming of mono-allelic choice throughout development. Most regions of the mammalian genome replicate both alleles in a synchronous manner, but some loci have been found to replicate asynchronously and the time of replication of each allele is different. Here the authors, by employing clonal mouse cells from a hybrid strain chart replication timing over the entire genome, using polymorphisms to distinguish between the paternal and maternal alleles.
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12
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Chandradoss KR, Chawla B, Dhuppar S, Nayak R, Ramachandran R, Kurukuti S, Mazumder A, Sandhu KS. CTCF-Mediated Genome Architecture Regulates the Dosage of Mitotically Stable Mono-allelic Expression of Autosomal Genes. Cell Rep 2020; 33:108302. [PMID: 33113374 DOI: 10.1016/j.celrep.2020.108302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 07/31/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
The mechanisms that guide the clonally stable random mono-allelic expression of autosomal genes remain enigmatic. We show that (1) mono-allelically expressed (MAE) genes are assorted and insulated from bi-allelically expressed (BAE) genes through CTCF-mediated chromatin loops; (2) the cell-type-specific dynamics of mono-allelic expression coincides with the gain and loss of chromatin insulator sites; (3) dosage of MAE genes is more sensitive to the loss of chromatin insulation than that of BAE genes; and (4) inactive alleles of MAE genes are significantly more insulated than active alleles and are de-repressed upon CTCF depletion. This alludes to a topology wherein the inactive alleles of MAE genes are insulated from the spatial interference of transcriptional states from the neighboring bi-allelic domains via CTCF-mediated loops. We propose that CTCF functions as a typical insulator on inactive alleles, but facilitates transcription through enhancer-linking on active allele of MAE genes, indicating widespread allele-specific regulatory roles of CTCF.
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Affiliation(s)
- Keerthivasan Raanin Chandradoss
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Bindia Chawla
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Shivnarayan Dhuppar
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Rakhee Nayak
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Rajesh Ramachandran
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India
| | - Sreenivasulu Kurukuti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research (TIFR) Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Kuljeet Singh Sandhu
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India.
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13
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Varrault A, Dubois E, Le Digarcher A, Bouschet T. Quantifying Genomic Imprinting at Tissue and Cell Resolution in the Brain. EPIGENOMES 2020; 4:21. [PMID: 34968292 PMCID: PMC8594728 DOI: 10.3390/epigenomes4030021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Imprinted genes are a group of ~150 genes that are preferentially expressed from one parental allele owing to epigenetic marks asymmetrically distributed on inherited maternal and paternal chromosomes. Altered imprinted gene expression causes human brain disorders such as Prader-Willi and Angelman syndromes and additional rare brain diseases. Research data principally obtained from the mouse model revealed how imprinted genes act in the normal and pathological brain. However, a better understanding of imprinted gene functions calls for building detailed maps of their parent-of-origin-dependent expression and of associated epigenetic signatures. Here we review current methods for quantifying genomic imprinting at tissue and cell resolutions, with a special emphasis on methods to detect parent-of-origin dependent expression and their applications to the brain. We first focus on bulk RNA-sequencing, the main method to detect parent-of-origin-dependent expression transcriptome-wide. We discuss the benefits and caveats of bulk RNA-sequencing and provide a guideline to use it on F1 hybrid mice. We then review methods for detecting parent-of-origin-dependent expression at cell resolution, including single-cell RNA-seq, genetic reporters, and molecular probes. Finally, we provide an overview of single-cell epigenomics technologies that profile additional features of genomic imprinting, including DNA methylation, histone modifications and chromatin conformation and their combination into sc-multimodal omics approaches, which are expected to yield important insights into genomic imprinting in individual brain cells.
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Affiliation(s)
- Annie Varrault
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Emeric Dubois
- Montpellier GenomiX (MGX), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France;
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France; (A.V.); (A.L.D.)
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14
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Martínez-Glez V, Tenorio J, Nevado J, Gordo G, Rodríguez-Laguna L, Feito M, de Lucas R, Pérez-Jurado LA, Ruiz Pérez VL, Torrelo A, Spinner NB, Happle R, Biesecker LG, Lapunzina P. A six-attribute classification of genetic mosaicism. Genet Med 2020; 22:1743-1757. [PMID: 32661356 PMCID: PMC8581815 DOI: 10.1038/s41436-020-0877-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Mosaicism denotes an individual who has at least two populations of cells with distinct genotypes that are derived from a single fertilized egg. Genetic variation among the cell lines can involve whole chromosomes, structural or copy number variants, small or single nucleotide variants, or epigenetic variants. The mutational events that underlie mosaic variants occur during mitotic cell divisions after fertilization and zygote formation. The initiating mutational event can occur in any types of cell at any time in development, leading to enormous variation in the distribution and phenotypic effect of mosaicism. A number of classification proposals have been put forward to classify genetic mosaicism into categories based on the location, pattern, and mechanisms of the disease. We here propose a new classification of genetic mosaicism that considers the affected tissue, the pattern and distribution of the mosaicism, the pathogenicity of the variant, the direction of the change (benign to pathogenic vs. pathogenic to benign), and the postzygotic mutational mechanism. The accurate and comprehensive categorization and subtyping of mosaicisms is important and has potential clinical utility to define the natural history of these disorders, tailor follow-up frequency and interventions, estimate recurrence risks, and guide therapeutic decisions.
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Affiliation(s)
- Víctor Martínez-Glez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| | - Jair Tenorio
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Gema Gordo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Lara Rodríguez-Laguna
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Marta Feito
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Raúl de Lucas
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra and Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Women's and Children's Hospital, South Australia Medical and Health Research Institute (SAHMRI) and University of Adelaide, Adelaide, SA, Australia
| | - Víctor L Ruiz Pérez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.,Instituto de Investigaciones Biomédicas de Madrid (CSIC-UAM), Madrid, Spain
| | - Antonio Torrelo
- Department of Pediatrics, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicines at The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rudolf Happle
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
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15
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Heskett MB, Smith LG, Spellman P, Thayer MJ. Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6. RNA (NEW YORK, N.Y.) 2020; 26:724-738. [PMID: 32144193 PMCID: PMC7266157 DOI: 10.1261/rna.073114.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
DNA replication occurs on mammalian chromosomes in a cell-type distinctive temporal order known as the replication timing program. We previously found that disruption of the noncanonical lncRNA genes ASAR6 and ASAR15 results in delayed replication timing and delayed mitotic chromosome condensation of human chromosomes 6 and 15, respectively. ASAR6 and ASAR15 display random monoallelic expression and display asynchronous replication between alleles that is coordinated with other random monoallelic genes on their respective chromosomes. Disruption of the expressed allele, but not the silent allele, of ASAR6 leads to delayed replication, activation of the previously silent alleles of linked monoallelic genes, and structural instability of human chromosome 6. In this report, we describe a second lncRNA gene (ASAR6-141) on human chromosome 6 that when disrupted results in delayed replication timing in cisASAR6-141 is subject to random monoallelic expression and asynchronous replication and is expressed from the opposite chromosome 6 homolog as ASAR6 ASAR6-141 RNA, like ASAR6 and ASAR15 RNAs, contains a high L1 content and remains associated with the chromosome territory where it is transcribed. Three classes of cis-acting elements control proper chromosome function in mammals: origins of replication, centromeres, and telomeres, which are responsible for replication, segregation, and stability of all chromosomes. Our work supports a fourth type of essential chromosomal element, the "Inactivation/Stability Center," which expresses ASAR lncRNAs responsible for proper replication timing, monoallelic expression, and structural stability of each chromosome.
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Affiliation(s)
- Michael B Heskett
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Leslie G Smith
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Paul Spellman
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Mathew J Thayer
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, USA
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16
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Wang CHY, Loignon C, Hudon C. Uncovering social and psychosocial health factors through participatory qualitative research with low-income adults in a suburb of Montreal, Quebec. BMJ Open 2020; 10:e030193. [PMID: 32051296 PMCID: PMC7045024 DOI: 10.1136/bmjopen-2019-030193] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES The association between social status and health is well established, but the psychosocial factors and mechanisms underlying this association are not fully understood. This study aims to identify and describe social and psychosocial factors that may harm the health of low-income adults. DESIGN Participatory qualitative research using a problem-posing method based on Freire's pedagogy. SETTING Community organisation in a low-income district in the metropolitan area of Montreal, in the province of Quebec, Canada. PARTICIPANTS Eight low-income adults using food bank services provided by the community organisation. Participants had to reside in the community organisation's service area, have insufficient income to cover living expenses, be aged 18 years or older, and be able to participate in group sessions. METHODS Eight weekly group sessions (average of 2.5 hours per session) were held using problem-posing method, which included activities such as presentation of representative stories or images and role-playing. Five additional sessions were held for thematic data analysis with participants. RESULTS A main factor identified as harming the health of participants was the dissonance between perceived current circumstances and the ideal of circumstances conceived early in life. This dissonance follows a loss or a failure to achieve the ideal of circumstances and generates profound malaise. Other main factors identified were the current circumstances as a social trap and the lack of love and support from an early age. CONCLUSIONS This study identifies a new psychosocial factor, namely, the dissonance between perceived current circumstances and the ideal of circumstances conceived early in life. Larger studies should examine the influence of this factor on health.
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Affiliation(s)
- Caroline H-Y Wang
- Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Centre de recherche Charles-Le Moyne-Saguenay-Lac-Saint-Jean sur les innovations en santé, Centre intégré de santé et de services sociaux de la Montérégie-Centre, Longueuil, Quebec, Canada
| | - Christine Loignon
- Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Centre de recherche Charles-Le Moyne-Saguenay-Lac-Saint-Jean sur les innovations en santé, Centre intégré de santé et de services sociaux de la Montérégie-Centre, Longueuil, Quebec, Canada
- Département de médecine de famille et de médecine d'urgence, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Catherine Hudon
- Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Département de médecine de famille et de médecine d'urgence, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
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17
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Julian CG. An Aptitude for Altitude: Are Epigenomic Processes Involved? Front Physiol 2019; 10:1397. [PMID: 31824328 PMCID: PMC6883803 DOI: 10.3389/fphys.2019.01397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/29/2019] [Indexed: 12/30/2022] Open
Abstract
In recent years, high-throughput genomic technologies and computational advancements have invigorated efforts to identify the molecular mechanisms regulating human adaptation to high altitude. Although exceptional progress regarding the identification of genomic regions showing evidence of recent positive selection has been made, many of the key “hypoxia tolerant” phenotypes of highland populations have not yet been linked to putative adaptive genetic variants. As a result, fundamental questions regarding the biological processes by which such adaptations are acquired remain unanswered. This Mini Review discusses the hypothesis that the epigenome works in coordination with underlying genomic sequence to govern adaptation to the chronic hypoxia of high altitude by influencing adaptive capacity and phenotypic variation under conditions of environmental hypoxia. Efforts to unravel the complex interactions between the genome, epigenome, and environmental exposures are essential to more fully appreciate the mechanisms underlying human adaptation to hypoxia.
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Affiliation(s)
- Colleen G Julian
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
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18
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Abstract
Evolutionary rates and strength of selection differ markedly between haploid and diploid genomes. Any genes expressed in a haploid state will be directly exposed to selection, whereas alleles in a diploid state may be partially or fully masked by a homologous allele. This difference may shape key evolutionary processes, including rates of adaptation and inbreeding depression, but also the evolution of sex chromosomes, heterochiasmy, and stable sex ratio biases. All diploid organisms carry haploid genomes, most notably the haploid genomes in gametes produced by every sexually reproducing eukaryote. Furthermore, haploid expression occurs in genes with monoallelic expression, in sex chromosomes, and in organelles, such as mitochondria and plastids. A comparison of evolutionary rates among these haploid genomes reveals striking parallels. Evidence suggests that haploid selection has the potential to shape evolution in predominantly diploid organisms, and taking advantage of the rapidly developing technologies, we are now in the position to quantify the importance of such selection on haploid genomes.
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Affiliation(s)
- Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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19
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Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T. Significant abundance of cis configurations of coding variants in diploid human genomes. Nucleic Acids Res 2019; 47:2981-2995. [PMID: 30698752 PMCID: PMC6451136 DOI: 10.1093/nar/gkz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
To fully understand human genetic variation and its functional consequences, the specific distribution of variants between the two chromosomal homologues of genes must be known. The 'phase' of variants can significantly impact gene function and phenotype. To assess patterns of phase at large scale, we have analyzed 18 121 autosomal genes in 1092 statistically phased genomes from the 1000 Genomes Project and 184 experimentally phased genomes from the Personal Genome Project. Here we show that genes with cis-configurations of coding variants are more frequent than genes with trans-configurations in a genome, with global cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all genomes in all populations. Moreover, we identified a large group of genes exhibiting cis-configurations of protein-changing variants in excess, so-called 'cis-abundant genes', and a smaller group of 'trans-abundant genes'. These two gene categories were functionally distinguishable, and exhibited strikingly different distributional patterns of protein-changing variants. Underlying these phenomena was a shared set of phase-sensitive genes of importance for adaptation and evolution. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their functional significance, highlighting the importance of phase for the interpretation of protein-coding genetic variation and gene function.
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Affiliation(s)
- Margret R Hoehe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Qing Mao
- Complete Genomics, Inc., San Jose, CA 95112, USA
| | - Brock A Peters
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - Radoje Drmanac
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Huebsch
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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20
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Pilvar D, Reiman M, Pilvar A, Laan M. Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy. Clin Epigenetics 2019; 11:94. [PMID: 31242935 PMCID: PMC6595585 DOI: 10.1186/s13148-019-0692-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/06/2019] [Indexed: 12/22/2022] Open
Abstract
Background Genomic imprinting, mediated by parent-of-origin-specific epigenetic silencing, adjusts the gene expression dosage in mammals. We aimed to clarify parental allelic expression in the human placenta for 396 claimed candidate imprinted genes and to assess the evidence for the proposed enrichment of imprinted expression in the placenta. The study utilized RNA-Seq-based transcriptome and genotyping data from 54 parental-placental samples representing the three trimesters of gestation, and term cases of preeclampsia, gestational diabetes, and fetal growth disturbances. Results Almost half of the targeted genes (n = 179; 45%) were either not transcribed or showed limited expression in the human placenta. After filtering for the presence of common exonic SNPs, adequacy of sequencing reads and informative families, 91 genes were retained (43 loci form Geneimprint database; 48 recently proposed genes). Only 11/91 genes (12.1%) showed confident signals of imprinting (binomial test, Bonferroni corrected P < 0.05; > 90% transcripts originating from one parental allele). The confirmed imprinted genes exhibit enriched placental expression (PHLDA2, H19, IGF2, MEST, ZFAT, PLAGL1, AIM1) or are transcribed additionally only in the adrenal gland (MEG3, RTL1, PEG10, DLK1). Parental monoallelic expression showed extreme stability across gestation and in term pregnancy complications. A distinct group of additional 14 genes exhibited a statistically significant bias in parental allelic proportions defined as having 65–90% of reads from one parental allele (e.g., KLHDC10, NLRP2, RHOBTB3, DNMT1). Molecular mechanisms behind biased parental expression are still to be clarified. However, 66 of 91 (72.5%) analyzed candidate imprinted genes showed no signals of deviation from biallelic expression. Conclusions As placental tissue is not included in The Genotype-Tissue Expression (GTEx) project, the study contributed to fill the gap in the knowledge concerning parental allelic expression. A catalog of parental allelic proportions and gene expression of analyzed loci across human gestation and in term pregnancy complications is provided as additional files. The study outcome suggested that true imprinting in the human placenta is restricted to well-characterized loci. High expression of imprinted genes during mid-pregnancy supports their critical role in developmental programming. Consistent with the data on other GTEx tissues, the number of human imprinted genes appears to be overestimated. Electronic supplementary material The online version of this article (10.1186/s13148-019-0692-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana Pilvar
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila Str, 19 50411, Tartu, Estonia
| | - Mario Reiman
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila Str, 19 50411, Tartu, Estonia
| | - Arno Pilvar
- Veeuss OÜ, Jaama tn 185-49, 50705, Tartu, Tartu, Estonia
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila Str, 19 50411, Tartu, Estonia.
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21
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Reinius B, Sandberg R. Reply to 'High prevalence of clonal monoallelic expression'. Nat Genet 2019; 50:1199-1200. [PMID: 30082784 DOI: 10.1038/s41588-018-0189-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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22
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Vigneau S, Vinogradova S, Savova V, Gimelbrant A. High prevalence of clonal monoallelic expression. Nat Genet 2019; 50:1198-1199. [PMID: 30082785 DOI: 10.1038/s41588-018-0188-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Sébastien Vigneau
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Svetlana Vinogradova
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Virginia Savova
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander Gimelbrant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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23
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Katsumata Y, Nelson PT, Estus S, Fardo DW. Translating Alzheimer's disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs. Neurobiol Aging 2019; 74:135-146. [PMID: 30448613 PMCID: PMC6331247 DOI: 10.1016/j.neurobiolaging.2018.10.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/24/2018] [Accepted: 10/14/2018] [Indexed: 12/12/2022]
Abstract
The International Genomics of Alzheimer's Project (IGAP) is a consortium for characterizing the genetic landscape of Alzheimer's disease (AD). The identified and/or confirmed 19 single-nucleotide polymorphisms (SNPs) associated with AD are located on non-coding DNA regions, and their functional impacts on AD are as yet poorly understood. We evaluated the roles of the IGAP SNPs by integrating data from many resources, based on whether the IGAP SNP was (1) a proxy for a coding SNP or (2) associated with altered mRNA transcript levels. For (1), we confirmed that 12 AD-associated coding common SNPs and five nonsynonymous rare variants are in linkage disequilibrium with the IGAP SNPs. For (2), the IGAP SNPs in CELF1 and MS4A6A were associated with expression of their neighboring genes, MYBPC3 and MS4A6A, respectively, in blood. The IGAP SNP in DSG2 was an expression quantitative trait loci (eQTL) for DLGAP1 and NETO1 in the human frontal cortex. The IGAP SNPs in ABCA7, CD2AP, and CD33 each acted as eQTL for AD-associated genes in brain. Our approach for identifying proxies and examining eQTL highlighted potentially impactful, novel gene regulatory phenomena pertinent to the AD phenotype.
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Affiliation(s)
- Yuriko Katsumata
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Peter T. Nelson
- Department of Pathology, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Steven Estus
- Department of Physiology, University of Kentucky, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | | | - David W. Fardo
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
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Sequence variation of necdin gene in Bovidae. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2018; 60:32. [PMID: 30598832 PMCID: PMC6302488 DOI: 10.1186/s40781-018-0191-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 12/10/2018] [Indexed: 11/28/2022]
Abstract
Background Necdin (NDN), a member of the melanoma antigen family showing imprinted pattern of expression, has been implicated as causing Prader-Willi symptoms, and known to participate in cellular growth, cellular migration and differentiation. The region where NDN is located has been associated to QTLs affecting reproduction and early growth in cattle, but location and functional analysis of the molecular mechanisms have not been established. Methods Here we report the sequence variation of the entire coding sequence from 72 samples of cattle, yak, buffalo, goat and sheep, and discuss its variation in Bovidae. Median-joining network analysis was used to analyze the variation found in the species. Synonymous and non-synonymous substitution rates were determined for the analysis of all the polymorphic sites. Phylogenetic analysis were carried out among the species of Bovidae to reconstruct their relationships. Results From the phylogenetic analysis with the consensus sequences of the studied Bovidae species, we found that only 11 of the 26 nucleotide changes that differentiate them produced amino acid changes. All the SNPs found in the cattle breeds were novel and showed similar percentages of nucleotides with non-synonymous substitutions at the N-terminal, MHD and C-terminal (12.3, 12.8 and 12.5%, respectively), and were much higher than the percentage of synonymous substitutions (2.5, 2.6 and 4.9%, respectively). Three mutations in cattle and one in sheep, detected in heterozygous individuals were predicted to be deleterious. Additionally, the analysis of the biochemical characteristics in the most common form of the proteins in each species show very little difference in molecular weight, pI, net charge, instability index, aliphatic index and GRAVY (Table 4) in the Bovidae species, except for sheep, which had a higher molecular weight, instability index and GRAVY. Conclusions There is sufficient variation in this gene within and among the studied species, and because NDN carry key functions in the organism, it can have effects in economically important traits in the production of these species. NDN sequence is phylogenetically informative in this group, thus we propose this gene as a phylogenetic marker to study the evolution and conservation in Bovidae.
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Graves JAM. Marsupial genomics meet marsupial reproduction. Reprod Fertil Dev 2018; 31:1181-1188. [PMID: 30482268 DOI: 10.1071/rd18234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/08/2018] [Indexed: 11/23/2022] Open
Abstract
We came from very different backgrounds, with different skills and interests. Marilyn Renfree was recognised as 'a giant of marsupial embryology'; I had spent my working life studying genes and chromosomes. We teamed up out of mutual respect (awe on my side) to form, with Des Cooper, the ARC Centre of Excellence in Kangaroo Genomics. This is the story of how our collaboration came to be, and what it has produced for our knowledge of some of the world's most remarkable animals.
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Platt EJ, Smith L, Thayer MJ. L1 retrotransposon antisense RNA within ASAR lncRNAs controls chromosome-wide replication timing. J Cell Biol 2017; 217:541-553. [PMID: 29288153 PMCID: PMC5800813 DOI: 10.1083/jcb.201707082] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/19/2017] [Accepted: 11/27/2017] [Indexed: 12/11/2022] Open
Abstract
Proper chromosome duplication is critical for genome integrity and normal cellular function. Platt et al. show that the lncRNA genes ASAR6 and ASAR15 control chromosome-wide replication timing via the antisense strand of L1 retrotransposons located within ASAR6 and ASAR15 RNAs. Mammalian cells replicate their chromosomes via a temporal replication program. The ASAR6 and ASAR15 genes were identified as loci that when disrupted result in delayed replication and condensation of entire human chromosomes. ASAR6 and ASAR15 are monoallelically expressed long noncoding RNAs that remain associated with the chromosome from which they are transcribed. The chromosome-wide effects of ASAR6 map to the antisense strand of an L1 retrotransposon within ASAR6 RNA, deletion or inversion of which delayed replication of human chromosome 6. Furthermore, ectopic integration of ASAR6 or ASAR15 transgenes into mouse chromosomes resulted in delayed replication and condensation, an increase in H3K27me3, coating of the mouse chromosome with ASAR RNA, and a loss of mouse Cot-1 RNA expression in cis. Targeting the antisense strand of the L1 within ectopically expressed ASAR6 RNA restored normal replication timing. Our results provide direct evidence that L1 antisense RNA plays a functional role in chromosome-wide replication timing of mammalian chromosomes.
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Affiliation(s)
- Emily J Platt
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
| | - Leslie Smith
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
| | - Mathew J Thayer
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
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von Mohr M, Kirsch LP, Fotopoulou A. The soothing function of touch: affective touch reduces feelings of social exclusion. Sci Rep 2017; 7:13516. [PMID: 29044137 PMCID: PMC5647341 DOI: 10.1038/s41598-017-13355-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/19/2017] [Indexed: 11/29/2022] Open
Abstract
The mammalian need for social proximity, attachment and belonging may have an adaptive and evolutionary value in terms of survival and reproductive success. Consequently, ostracism may induce strong negative feelings of social exclusion. Recent studies suggest that slow, affective touch, which is mediated by a separate, specific C tactile neurophysiological system than faster, neutral touch, modulates the perception of physical pain. However, it remains unknown whether slow, affective touch, can also reduce feelings of social exclusion, a form of social pain. Here, we employed a social exclusion paradigm, namely the Cyberball task (N = 84), to examine whether the administration of slow, affective touch may reduce the negative feelings of ostracism induced by the social exclusion manipulations of the Cyberball task. As predicted, the provision of slow-affective, as compared to fast-neutral, touch led to a specific decrease in feelings of social exclusion, beyond general mood effects. These findings point to the soothing function of slow, affective touch, particularly in the context of social separation or rejection, and suggest a specific relation between affective touch and social bonding.
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Affiliation(s)
- Mariana von Mohr
- Research Department of Clinical, Educational and Health Psychology, University College London, London, United Kingdom.
| | - Louise P Kirsch
- Research Department of Clinical, Educational and Health Psychology, University College London, London, United Kingdom
| | - Aikaterini Fotopoulou
- Research Department of Clinical, Educational and Health Psychology, University College London, London, United Kingdom
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Mining Novel Candidate Imprinted Genes Using Genome-Wide Methylation Screening and Literature Review. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1020013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Abstract
The Modern Evolutionary Synthesis (MS) forged in the mid-twentieth century was built on a notion of heredity that excluded soft inheritance, the inheritance of the effects of developmental modifications. However, the discovery of molecular mechanisms that generate random and developmentally induced epigenetic variations is leading to a broadening of the notion of biological heredity that has consequences for ideas about evolution. After presenting some old challenges to the MS that were raised, among others, by Karl Popper, I discuss recent research on epigenetic inheritance, which provides experimental and theoretical support for these challenges. There is now good evidence that epigenetic inheritance is ubiquitous and is involved in adaptive evolution and macroevolution. I argue that the many evolutionary consequences of epigenetic inheritance open up new research areas and require the extension of the evolutionary synthesis beyond the current neo-Darwinian model.
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Affiliation(s)
- Eva Jablonka
- The Cohn Institute for the History and Philosophy of Science and Ideas, Tel-Aviv University, Tel-Aviv 69978, Israel
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Chuang TJ, Tseng YH, Chen CY, Wang YD. Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios. Sci Rep 2017; 7:7038. [PMID: 28765567 PMCID: PMC5539102 DOI: 10.1038/s41598-017-07514-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/23/2017] [Indexed: 11/23/2022] Open
Abstract
Genomic imprinting is an important epigenetic process that silences one of the parentally-inherited alleles of a gene and thereby exhibits allelic-specific expression (ASE). Detection of human imprinting events is hampered by the infeasibility of the reciprocal mating system in humans and the removal of ASE events arising from non-imprinting factors. Here, we describe a pipeline with the pattern of reciprocal allele descendants (RADs) through genotyping and transcriptome sequencing data across independent parent-offspring trios to discriminate between varied types of ASE (e.g., imprinting, genetic variation-dependent ASE, and random monoallelic expression (RME)). We show that the vast majority of ASE events are due to sequence-dependent genetic variant, which are evolutionarily conserved and may themselves play a cis-regulatory role. Particularly, 74% of non-RAD ASE events, even though they exhibit ASE biases toward the same parentally-inherited allele across different individuals, are derived from genetic variation but not imprinting. We further show that the RME effect may affect the effectiveness of the population-based method for detecting imprinting events and our pipeline can help to distinguish between these two ASE types. Taken together, this study provides a good indicator for categorization of different types of ASE, opening up this widespread and complex mechanism for comprehensive characterization.
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Affiliation(s)
| | | | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Da Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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Revealing allele-specific gene expression by single-cell transcriptomics. Int J Biochem Cell Biol 2017; 90:155-160. [PMID: 28578186 DOI: 10.1016/j.biocel.2017.05.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/21/2022]
Abstract
Single-cell sequencing has emerged as a revolutionary method that reveals biological processes with unprecedented resolution and scale, and has already greatly impacted biology and medicine. To investigate processes such as alternative splicing, novel exon detection and allele-specific expression (ASE), full-length based single-cell RNA-seq methods are required for broad sequence coverage and single nucleotide polymorphism (SNP) identification. In this review, we revisit recent achievements from studies that used single-cell RNA-seq to advance our understanding of ASE in the context of both autosomal and X-chromosome genes. We also recapitulate useful bioinformatic tools developed to identify haplotype phase.
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Whitburn LY, Jones LE, Davey MA, Small R. The meaning of labour pain: how the social environment and other contextual factors shape women's experiences. BMC Pregnancy Childbirth 2017; 17:157. [PMID: 28558667 PMCID: PMC5450354 DOI: 10.1186/s12884-017-1343-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 05/24/2017] [Indexed: 01/30/2023] Open
Abstract
Background The majority of women experience pain during labour and childbirth, however not all women experience it in the same way. In order to develop a more complete understanding of labour pain, this study aimed to examine women’s experiences within the perspective of modern pain science. A more complete understanding of this phenomenon can then guide the development of interventions to enhance women’s experiences and potentially reduce their need for pharmacological intervention. Methods A qualitative study was conducted using phenomenology as the theoretical framework. Data were collected from 21 nulliparous women, birthing at one of two large maternity services, through face-to-face interviews and written questionnaires. Data were analysed using an Interpretative Phenomenological Analysis approach. Results The data from this study suggest that a determining factor of a woman’s experience of pain during labour is the meaning she ascribes to it. When women interpret the pain as productive and purposeful, it is associated with positive cognitions and emotions, and they are more likely to feel they can cope. Alternatively, when women interpret the pain as threatening, it is associated with negative cognitions and emotions and they tend to feel they need help from external methods of pain control. The social environment seems particularly important in shaping a woman’s pain experience by influencing her interpretation of the context of the pain, and in doing so can change its meaning. The context and social environment are dynamic and can also change throughout labour. Conclusion A determining factor in a woman’s experience of pain during labour is its perceived meaning which can then influence how the woman responds to the pain. The meaning of the pain is shaped by the social environment and other contextual factors within which it is experienced. Focussed promotion of labour pain as a productive and purposeful pain and efforts to empower women to utilise their inner capacity to cope, as well as careful attention to women’s cognitions and the social environment around them may improve women’s experiences of labour pain and decrease their need for pain interventions. Electronic supplementary material The online version of this article (doi:10.1186/s12884-017-1343-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Y Whitburn
- School of Life Sciences & Judith Lumley Centre, La Trobe University, Bundoora, Victoria, 3086, Australia.
| | - Lester E Jones
- Judith Lumley Centre, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Mary-Ann Davey
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, 3800, Australia
| | - Rhonda Small
- Judith Lumley Centre, La Trobe University, Bundoora, Victoria, 3086, Australia
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Abstract
Monoallelic expression not due to cis-regulatory sequence polymorphism poses an intriguing problem in epigenetics because it requires the unequal treatment of two segments of DNA that are present in the same nucleus and that can indeed have absolutely identical sequences. Here, I focus on a few recent developments in the field of monoallelic expression that are of particular interest and raise interesting questions for future work. One development is regarding analyses of imprinted genes, in which recent work suggests the possibility that intriguing networks of imprinted genes exist and are important for genetic and physiological studies. Another issue that has been raised in recent years by a number of publications is the question of how skewed allelic expression should be for it to be designated as monoallelic expression and, further, what methods are appropriate or inappropriate for analyzing genomic data to examine allele-specific expression. Perhaps the most exciting recent development in mammalian monoallelic expression is a clever and carefully executed analysis of genetic diversity of autosomal genes subject to random monoallelic expression (RMAE), which provides compelling evidence for distinct evolutionary forces acting on random monoallelically expressed genes.
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Affiliation(s)
- Andrew Chess
- Department of Genetics and Genomic Sciences, Department of Developmental and Regenerative Biology, Fishberg Department of Neuroscience, and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574;
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The push of social pain: Does rejection's sting motivate subsequent social reconnection? COGNITIVE AFFECTIVE & BEHAVIORAL NEUROSCIENCE 2017; 16:541-50. [PMID: 26912270 DOI: 10.3758/s13415-016-0412-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Physical pain motivates the healing of somatic injuries, yet it remains unknown whether social pain serves a similarly reparative function toward social injuries. Given the substantial overlap between physical and social pain, we predicted that social pain would mediate the effect of rejection on greater motivation for social reconnection and affiliative behavior toward rejecters. In Study 1, the effect of rejection on an increased need to belong was mediated by reports of more intense social pain. In Study 2, three neural signatures of social pain (i.e., activity in the dorsal anterior cingulate cortex, left and right anterior insula during social rejection), each predicted greater behavioral proximity to rejecters. Our findings reify the overlap between social and physical pain. Furthermore, these results are some of the first to demonstrate the reparative nature of social pain and lend insight into how this process may be harnessed to promote postrejection reconnection.
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Lysine-specific demethylase-1 (LSD1) depletion disrupts monogenic and monoallelic odorant receptor (OR) expression in an olfactory neuronal cell line. Mol Cell Neurosci 2017; 82:1-11. [PMID: 28414096 DOI: 10.1016/j.mcn.2017.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 04/05/2017] [Accepted: 04/13/2017] [Indexed: 11/22/2022] Open
Abstract
Function of the mammalian olfactory system depends on specialized olfactory sensory neurons (OSNs) that each express only one allele ("monoallelic") of one odorant receptor (OR) gene ("monogenic"). The lysine-specific demethylase-1 (LSD1) protein removes activating H3K4 or silencing H3K9 methylation marks in a variety of developmental contexts, and is thought to be important for proper OR regulation. Most of the focus in the field has been on a potential "activating" function for LSD1; e.g., in the demethylation of H3K9 associated with the expressed OR allele. Here we show that depletion of LSD1 in an immortalized olfactory-placode-derived cell line (OP6) results in multigenic and multiallelic OR transcription per cell, while not seemingly disrupting the ability of these cells to activate new OR genes during clonal expansion. These results are consistent with LSD1 having a role in silencing additional OR alleles, as opposed to being required for the activation of OR alleles, within the OP6 cellular context.
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Deonovic B, Wang Y, Weirather J, Wang XJ, Au KF. IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing. Nucleic Acids Res 2017; 45:e32. [PMID: 27899656 PMCID: PMC5952581 DOI: 10.1093/nar/gkw1076] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/20/2016] [Accepted: 10/26/2016] [Indexed: 12/14/2022] Open
Abstract
Allele-specific expression (ASE) is a fundamental problem in studying gene regulation and diploid transcriptome profiles, with two key challenges: (i) haplotyping and (ii) estimation of ASE at the gene isoform level. Existing ASE analysis methods are limited by a dependence on haplotyping from laborious experiments or extra genome/family trio data. In addition, there is a lack of methods for gene isoform level ASE analysis. We developed a tool, IDP-ASE, for full ASE analysis. By innovative integration of Third Generation Sequencing (TGS) long reads with Second Generation Sequencing (SGS) short reads, the accuracy of haplotyping and ASE quantification at the gene and gene isoform level was greatly improved as demonstrated by the gold standard data GM12878 data and semi-simulation data. In addition to methodology development, applications of IDP-ASE to human embryonic stem cells and breast cancer cells indicate that the imbalance of ASE and non-uniformity of gene isoform ASE is widespread, including tumorigenesis relevant genes and pluripotency markers. These results show that gene isoform expression and allele-specific expression cooperate to provide high diversity and complexity of gene regulation and expression, highlighting the importance of studying ASE at the gene isoform level. Our study provides a robust bioinformatics solution to understand ASE using RNA sequencing data only.
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Affiliation(s)
- Benjamin Deonovic
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Yunhao Wang
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
- Key laboratory of Genetics Network Biology, Collaborative Innovation Center of Genetics and Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jason Weirather
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Xiu-Jie Wang
- Key laboratory of Genetics Network Biology, Collaborative Innovation Center of Genetics and Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kin Fai Au
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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Huang WC, Ferris E, Cheng T, Hörndli CS, Gleason K, Tamminga C, Wagner JD, Boucher KM, Christian JL, Gregg C. Diverse Non-genetic, Allele-Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain. Neuron 2017; 93:1094-1109.e7. [PMID: 28238550 PMCID: PMC5774018 DOI: 10.1016/j.neuron.2017.01.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 11/27/2016] [Accepted: 01/30/2017] [Indexed: 01/19/2023]
Abstract
Interactions between genetic and epigenetic effects shape brain function, behavior, and the risk for mental illness. Random X inactivation and genomic imprinting are epigenetic allelic effects that are well known to influence genetic architecture and disease risk. Less is known about the nature, prevalence, and conservation of other potential epigenetic allelic effects in vivo in the mouse and primate brain. Here we devise genomics, in situ hybridization, and mouse genetics strategies to uncover diverse allelic effects in the brain that are not caused by imprinting or genetic variation. We found allelic effects that are developmental stage and cell type specific, that are prevalent in the neonatal brain, and that cause mosaics of monoallelic brain cells that differentially express wild-type and mutant alleles for heterozygous mutations. Finally, we show that diverse non-genetic allelic effects that impact mental illness risk genes exist in the macaque and human brain. Our findings have potential implications for mammalian brain genetics. VIDEO ABSTRACT.
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Affiliation(s)
- Wei-Chao Huang
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Elliott Ferris
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Tong Cheng
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Cornelia Stacher Hörndli
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kelly Gleason
- Department of Psychiatry, UT Southwestern, Dallas, TX 75390-9127, USA
| | - Carol Tamminga
- Department of Psychiatry, UT Southwestern, Dallas, TX 75390-9127, USA
| | - Janice D Wagner
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Kenneth M Boucher
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Cancer Biostatistics Shared Resource, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jan L Christian
- Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Christopher Gregg
- Robertson Neuroscience Investigator, New York Stem Cell Foundation, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Departments of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Archer LK, Frame FM, Maitland NJ. Stem cells and the role of ETS transcription factors in the differentiation hierarchy of normal and malignant prostate epithelium. J Steroid Biochem Mol Biol 2017; 166:68-83. [PMID: 27185499 DOI: 10.1016/j.jsbmb.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/25/2016] [Accepted: 05/07/2016] [Indexed: 12/18/2022]
Abstract
Prostate cancer is the most common cancer of men in the UK and accounts for a quarter of all new cases. Although treatment of localised cancer can be successful, there is no cure for patients presenting with invasive prostate cancer and there are less treatment options. They are generally treated with androgen-ablation therapies but eventually the tumours become hormone resistant and patients develop castration-resistant prostate cancer (CRPC) for which there are no further successful or curative treatments. This highlights the need for new treatment strategies. In order to prevent prostate cancer recurrence and treatment resistance, all the cell populations in a heterogeneous prostate tumour must be targeted, including the rare cancer stem cell (CSC) population. The ETS transcription factor family members are now recognised as a common feature in multiple cancers including prostate cancer; with aberrant expression, loss of tumour suppressor function, inactivating mutations and the formation of fusion genes observed. Most notably, the TMPRSS2-ERG gene fusion is present in approximately 50% of prostate cancers and in prostate CSCs. However, the role of other ETS transcription factors in prostate cancer is less well understood. This review will describe the prostate epithelial cell hierarchy and discuss the evidence behind prostate CSCs and their inherent resistance to conventional cancer therapies. The known and proposed roles of the ETS family of transcription factors in prostate epithelial cell differentiation and regulation of the CSC phenotype will be discussed, as well as how they might be targeted for therapy.
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Affiliation(s)
- Leanne K Archer
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Fiona M Frame
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Norman J Maitland
- Cancer Research Unit, Department of Biology, University of York, York, YO10 5DD, United Kingdom.
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40
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Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells. Nat Genet 2017; 49:377-386. [PMID: 28112738 DOI: 10.1038/ng.3769] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/14/2016] [Indexed: 12/12/2022]
Abstract
We developed an allele-specific assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to genotype and profile active regulatory DNA across the genome. Using a mouse hybrid F1 system, we found that monoallelic DNA accessibility across autosomes was pervasive, developmentally programmed and composed of several patterns. Genetically determined accessibility was enriched at distal enhancers, but random monoallelically accessible (RAMA) elements were enriched at promoters and may act as gatekeepers of monoallelic mRNA expression. Allelic choice at RAMA elements was stable across cell generations and bookmarked through mitosis. RAMA elements in neural progenitor cells were biallelically accessible in embryonic stem cells but premarked with bivalent histone modifications; one allele was silenced during differentiation. Quantitative analysis indicated that allelic choice at the majority of RAMA elements is consistent with a stochastic process; however, up to 30% of RAMA elements may deviate from the expected pattern, suggesting a regulated or counting mechanism.
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Liu T, Li H, Ding Y, Qi Y, Gao Y, Song A, Shen J, Qiu L. Genome-wide gene expression patterns in dikaryon of the basidiomycete fungus Pleurotus ostreatus. Braz J Microbiol 2017; 48:380-390. [PMID: 28089161 PMCID: PMC5470450 DOI: 10.1016/j.bjm.2016.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/20/2016] [Indexed: 01/10/2023] Open
Abstract
Dikarya is a subkingdom of fungi that includes Ascomycota and Basidiomycota. The gene expression patterns of dikaryon are poorly understood. In this study, we bred a dikaryon DK13×3 by mating monokaryons MK13 and MK3, which were from the basidiospores of Pleurotus ostreatus TD300. Using RNA-Seq, we obtained the transcriptomes of the three strains. We found that the total transcript numbers in the transcriptomes of the three strains were all more than ten thousand, and the expression profile in DK13×3 was more similar to MK13 than MK3. However, the genes involved in macromolecule utilization, cellular material synthesis, stress-resistance and signal transduction were much more up-regulated in the dikaryon than its constituent monokaryons. All possible modes of differential gene expression, when compared to constituent monokaryons, including the presence/absence variation, and additivity/nonadditivity gene expression in the dikaryon may contribute to heterosis. By sequencing the urease gene poure sequences and mRNA sequences, we identified the monoallelic expression of the poure gene in the dikaryon, and its transcript was from the parental monokaryon MK13. Furthermore, we discovered RNA editing in the poure gene mRNA of the three strains. These results suggest that the gene expression patterns in dikaryons should be similar to that of diploids during vegetative growth.
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Affiliation(s)
- Tianxiang Liu
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Huiru Li
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Yatong Ding
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Yuancheng Qi
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Yuqian Gao
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Andong Song
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Jinwen Shen
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China
| | - Liyou Qiu
- Henan Agricultural University, College of Life Sciences, Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Zhengzhou, China.
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Hill EM, Hunt L, Duryea DG. Evolved Vulnerability to Addiction: The Problem of Opiates. EVOLUTIONARY PSYCHOLOGY 2017. [DOI: 10.1007/978-3-319-60576-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Mironov AA. A model of regulation of monoallelic gene expression. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Transcriptome Profiling in Rat Inbred Strains and Experimental Cross Reveals Discrepant Genetic Architecture of Genome-Wide Gene Expression. G3-GENES GENOMES GENETICS 2016; 6:3671-3683. [PMID: 27646706 PMCID: PMC5100866 DOI: 10.1534/g3.116.033274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
To test the impact of genetic heterogeneity on cis- and trans-mediated mechanisms of gene expression regulation, we profiled the transcriptome of adipose tissue in 20 inbred congenic strains derived from diabetic Goto-Kakizaki (GK) rats and Brown-Norway (BN) controls, which contain well-defined blocks (1-183 Mb) of genetic polymorphisms, and in 123 genetically heterogeneous rats of an (GK × BN)F2 offspring. Within each congenic we identified 73-1351 differentially expressed genes (DEGs), only 7.7% of which mapped within the congenic blocks, and which may be regulated in cis The remainder localized outside the blocks, and therefore must be regulated in trans Most trans-regulated genes exhibited approximately twofold expression changes, consistent with monoallelic expression. Altered biological pathways were replicated between congenic strains sharing blocks of genetic polymorphisms, but polymorphisms at different loci also had redundant effects on transcription of common distant genes and pathways. We mapped 2735 expression quantitative trait loci (eQTL) in the F2 cross, including 26% predominantly cis-regulated genes, which validated DEGs in congenic strains. A hotspot of >300 eQTL in a 10 cM region of chromosome 1 was enriched in DEGs in a congenic strain. However, many DEGs among GK, BN and congenic strains did not replicate as eQTL in F2 hybrids, demonstrating distinct mechanisms of gene expression when alleles segregate in an outbred population or are fixed homozygous across the entire genome or in short genomic regions. Our analysis provides conceptual advances in our understanding of the complex architecture of genome expression and pathway regulation, and suggests a prominent impact of epistasis and monoallelic expression on gene transcription.
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Weird mammals provide insights into the evolution of mammalian sex chromosomes and dosage compensation. J Genet 2016; 94:567-74. [PMID: 26690510 DOI: 10.1007/s12041-015-0572-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The deep divergence of mammalian groups 166 and 190 million years ago (MYA) provide genetic variation to explore the evolution of DNA sequence, gene arrangement and regulation of gene expression in mammals. With encouragement from the founder of the field, Mary Lyon, techniques in cytogenetics and molecular biology were progressively adapted to characterize the sex chromosomes of kangaroos and other marsupials, platypus and echidna-and weird rodent species. Comparative gene mapping reveals the process of sex chromosome evolution from their inception 190 MYA (they are autosomal in platypus) to their inevitable end (the Y has disappeared in two rodent lineages). Our X and Y are relatively young, getting their start with the evolution of the sex-determining SRY gene, which triggered progressive degradation of the Y chromosome. Even more recently, sex chromosomes of placental mammals fused with an autosomal region which now makes up most of the Y. Exploration of gene activity patterns over four decades showed that dosage compensation via X-chromosome inactivation is unique to therian mammals, and that this whole chromosome control process is different in marsupials and absent in monotremes and reptiles, and birds. These differences can be exploited to deduce how mammalian sex chromosomes and epigenetic silencing evolved.
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Will GJ, van Lier PAC, Crone EA, Güroğlu B. Chronic Childhood Peer Rejection is Associated with Heightened Neural Responses to Social Exclusion During Adolescence. JOURNAL OF ABNORMAL CHILD PSYCHOLOGY 2016; 44:43-55. [PMID: 25758671 PMCID: PMC4715124 DOI: 10.1007/s10802-015-9983-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This functional Magnetic Resonance Imaging (fMRI) study examined subjective and neural responses to social exclusion in adolescents (age 12-15) who either had a stable accepted (n = 27; 14 males) or a chronic rejected (n = 19; 12 males) status among peers from age 6 to 12. Both groups of adolescents reported similar increases in distress after being excluded in a virtual ball-tossing game (Cyberball), but adolescents with a history of chronic peer rejection showed higher activity in brain regions previously linked to the detection of, and the distress caused by, social exclusion. Specifically, compared with stably accepted adolescents, chronically rejected adolescents displayed: 1) higher activity in the dorsal anterior cingulate cortex (dACC) during social exclusion and 2) higher activity in the dACC and anterior prefrontal cortex when they were incidentally excluded in a social interaction in which they were overall included. These findings demonstrate that chronic childhood peer rejection is associated with heightened neural responses to social exclusion during adolescence, which has implications for understanding the processes through which peer rejection may lead to adverse effects on mental health over time.
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Affiliation(s)
- Geert-Jan Will
- Institute of Psychology, Leiden University, Wassenaarseweg 52, 2333, AK, Leiden, The Netherlands. .,Leiden Institute for Brain and Cognition (LIBC), Leiden University Medical Center, P.O. Box 9600, 2300, RC, Leiden, The Netherlands.
| | - Pol A C van Lier
- Department of Developmental Psychology, VU University, Van der Boechorststraat 1, 1081, BT, Amsterdam, The Netherlands
| | - Eveline A Crone
- Institute of Psychology, Leiden University, Wassenaarseweg 52, 2333, AK, Leiden, The Netherlands.,Leiden Institute for Brain and Cognition (LIBC), Leiden University Medical Center, P.O. Box 9600, 2300, RC, Leiden, The Netherlands.,Department of Psychology, University of Amsterdam, Weesperplein 4, 1018 XA, Amsterdam, The Netherlands
| | - Berna Güroğlu
- Institute of Psychology, Leiden University, Wassenaarseweg 52, 2333, AK, Leiden, The Netherlands.,Leiden Institute for Brain and Cognition (LIBC), Leiden University Medical Center, P.O. Box 9600, 2300, RC, Leiden, The Netherlands
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Jeffries AR, Uwanogho DA, Cocks G, Perfect LW, Dempster E, Mill J, Price J. Erasure and reestablishment of random allelic expression imbalance after epigenetic reprogramming. RNA (NEW YORK, N.Y.) 2016; 22:1620-1630. [PMID: 27539784 PMCID: PMC5029458 DOI: 10.1261/rna.058347.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Clonal level random allelic expression imbalance and random monoallelic expression provides cellular heterogeneity within tissues by modulating allelic dosage. Although such expression patterns have been observed in multiple cell types, little is known about when in development these stochastic allelic choices are made. We examine allelic expression patterns in human neural progenitor cells before and after epigenetic reprogramming to induced pluripotency, observing that loci previously characterized by random allelic expression imbalance (0.63% of expressed genes) are generally reset to a biallelic state in induced pluripotent stem cells (iPSCs). We subsequently neuralized the iPSCs and profiled isolated clonal neural stem cells, observing that significant random allelic expression imbalance is reestablished at 0.65% of expressed genes, including novel loci not found to show allelic expression imbalance in the original parental neural progenitor cells. Allelic expression imbalance was associated with altered DNA methylation across promoter regulatory regions, with clones characterized by skewed allelic expression being hypermethylated compared to their biallelic sister clones. Our results suggest that random allelic expression imbalance is established during lineage commitment and is associated with increased DNA methylation at the gene promoter.
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Affiliation(s)
- Aaron Richard Jeffries
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Dafe Aghogho Uwanogho
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Graham Cocks
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Leo William Perfect
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Emma Dempster
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
| | - Jack Price
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, United Kingdom
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Reinius B, Mold JE, Ramsköld D, Deng Q, Johnsson P, Michaëlsson J, Frisén J, Sandberg R. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. Nat Genet 2016; 48:1430-1435. [PMID: 27668657 PMCID: PMC5117254 DOI: 10.1038/ng.3678] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/29/2016] [Indexed: 12/16/2022]
Abstract
Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here we used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and freshly isolated human CD8+ T cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells' transcriptomes, with levels dependent on the cells' transcriptional activity. Notably, clonal aRME was detected, but it was surprisingly scarce (<1% of genes) and mainly affected the most weakly expressed genes. Consequently, the overwhelming majority of aRME occurs transiently within individual cells, and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells.
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Affiliation(s)
- Björn Reinius
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Daniel Ramsköld
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Qiaolin Deng
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Per Johnsson
- Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden
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Goodrich L, Panning B, Leung KN. Activators and repressors: A balancing act for X-inactivation. Semin Cell Dev Biol 2016; 56:3-8. [DOI: 10.1016/j.semcdb.2016.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/06/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
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