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Grzymski JJ, Elhanan G, Morales Rosado JA, Smith E, Schlauch KA, Read R, Rowan C, Slotnick N, Dabe S, Metcalf WJ, Lipp B, Reed H, Sharma L, Levin E, Kao J, Rashkin M, Bowes J, Dunaway K, Slonim A, Washington N, Ferber M, Bolze A, Lu JT. Population genetic screening efficiently identifies carriers of autosomal dominant diseases. Nat Med 2020; 26:1235-1239. [DOI: 10.1038/s41591-020-0982-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 06/12/2020] [Indexed: 01/10/2023]
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Rashkin MD, Bowes J, Dunaway K, Dhaliwal J, Loomis E, Riffle S, Washington NL, Ziegler C, Lu J, Levin E. Genetic counseling, 2030: An on-demand service tailored to the needs of a price conscious, genetically literate, and busy world. J Genet Couns 2020; 28:456-465. [PMID: 30964579 DOI: 10.1002/jgc4.1123] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022]
Abstract
The practice of genetic counseling is going to be impacted by the public's expectation that goods, services, information, and experiences happen on demand, wherever and whenever people want them. Building from trends that are currently taking shape, this article looks just over a decade into the future-to 2030-to provide a description of how the field of genetics and genetic counseling will be changed, as well as advice for genetic counselors for how to prepare. We build from the prediction that a large portion of the general public will have access to their digitized whole genome sequence anytime, any place, on any device. We focus on five topics downstream of this prediction: public health, personal autonomy, polygenic scores (PGS), evolving clinical practices, and genetic privacy.
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Affiliation(s)
| | | | | | | | | | | | | | | | - James Lu
- Helix Opco, LLC, San Carlos, California
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Yokoyama AS, Dunaway K, Rutkowsky J, Rutledge JC, Milenkovic D. Chronic consumption of a western diet modifies the DNA methylation profile in the frontal cortex of mice. Food Funct 2018; 9:1187-1198. [PMID: 29372223 DOI: 10.1039/c7fo01602f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In our previous work in mice, we have shown that chronic consumption of a Western diet (WD; 42% kcal fat, 0.2% total cholesterol and 34% sucrose) is correlated with impaired cognitive function. Cognitive decline has also been associated with alterations in DNA methylation. Additionally, although there have been many studies analyzing the effect of maternal consumption of a WD on DNA methylation in the offspring, few studies have analyzed how an individual's consumption of a WD can impact his/her DNA methylation. Since the frontal cortex is involved in the regulation of cognitive function and is often affected in cases of cognitive decline, this study aimed to examine how chronic consumption of a WD affects DNA methylation in the frontal cortex of mice. Eight-week-old male mice were fed either a control diet (CD) or a WD for 12 weeks, after which time alterations in DNA methylation were analyzed. Assessment of global DNA methylation in the frontal cortex using dot blot analysis revealed that there was a decrease in global DNA methylation in the WD-fed mice compared with the CD-fed mice. Bioinformatic analysis identified several networks and pathways containing genes displaying differential methylation, particularly those involved in metabolism, cell adhesion and cytoskeleton integrity, inflammation and neurological function. In conclusion, the results from this study suggest that consumption of a WD alters DNA methylation in the frontal cortex of mice and could provide one of the mechanisms by which consumption of a WD impairs cognitive function.
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Affiliation(s)
- Amy S Yokoyama
- Department of Internal Medicine, Division of Cardiovascular Medicine, School of Medicine, University of California Davis, Davis, California 95616, USA.
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Lopez SJ, Dunaway K, Islam MS, Mordaunt C, Vogel Ciernia A, Meguro-Horike M, Horike SI, Segal DJ, LaSalle JM. UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons. Epigenetics 2017; 12:982-990. [PMID: 28925810 PMCID: PMC5788436 DOI: 10.1080/15592294.2017.1376151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of genes in neurodevelopmental disorders that lead to social and cognitive phenotypes is a complex, multilayered process involving both genetics and epigenetics. Parent-of-origin effects of deletion and duplication of the 15q11-q13 locus leading to Angelman, Prader-Willi, and Dup15q syndromes are due to imprinted genes, including UBE3A, which is maternally expressed exclusively in neurons. UBE3A encodes a ubiquitin E3 ligase protein with multiple downstream targets, including RING1B, which in turn monoubiquitinates histone variant H2A.Z. To understand the impact of neuronal UBE3A levels on epigenome-wide marks of DNA methylation, histone variant H2A.Z positioning, active H3K4me3 promoter marks, and gene expression, we took a multi-layered genomics approach. We performed an siRNA knockdown of UBE3A in two human neuroblastoma cell lines, including parental SH-SY5Y and the SH(15M) model of Dup15q. Genes differentially methylated across cells with differing UBE3A levels were enriched for functions in gene regulation, DNA binding, and brain morphology. Importantly, we found that altering UBE3A levels had a profound epigenetic effect on the methylation levels of up to half of known imprinted genes. Genes with differential H2A.Z peaks in SH(15M) compared to SH-SY5Y were enriched for ubiquitin and protease functions and associated with autism, hypoactivity, and energy expenditure. Together, these results support a genome-wide epigenetic consequence of altered UBE3A levels in neurons and suggest that UBE3A regulates an imprinted gene network involving DNA methylation patterning and H2A.Z deposition.
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Affiliation(s)
- S Jesse Lopez
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
| | - Keith Dunaway
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
| | - M Saharul Islam
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Charles Mordaunt
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Annie Vogel Ciernia
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA
| | - Makiko Meguro-Horike
- f Advanced Science Research Center , Kanazawa University , 13-1 Takaramachi, Kanazawa , Ishikawa , Japan
| | - Shin-Ichi Horike
- f Advanced Science Research Center , Kanazawa University , 13-1 Takaramachi, Kanazawa , Ishikawa , Japan
| | - David J Segal
- b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA.,e Biochemistry and Molecular Medicine , University of California , Davis , CA , USA
| | - Janine M LaSalle
- a Medical Immunology and Microbiology , University of California , Davis , CA , USA.,b Genome Center , University of California , Davis , CA , USA.,c MIND Institute, University of California , Davis , CA , USA.,d Integrative Genetics and Genomics , University of California , Davis , CA , USA
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Hough SH, Kancleris K, Brody L, Humphryes-Kirilov N, Wolanski J, Dunaway K, Ajetunmobi A, Dillard V. Erratum to: Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments. BMC Bioinformatics 2017; 18:202. [PMID: 28376719 PMCID: PMC5379749 DOI: 10.1186/s12859-017-1618-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Soren H Hough
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK.
| | - Kris Kancleris
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
| | - Leigh Brody
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
| | | | - Joseph Wolanski
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
| | - Keith Dunaway
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
| | | | - Victor Dillard
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
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Hough SH, Kancleris K, Brody L, Humphryes-Kirilov N, Wolanski J, Dunaway K, Ajetunmobi A, Dillard V. Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments. BMC Bioinformatics 2017; 18:167. [PMID: 28288556 PMCID: PMC5348774 DOI: 10.1186/s12859-017-1581-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Guide Picker ( https://www.deskgen.com/guide-picker/ ) serves as a meta tool for designing CRISPR experiments by presenting ten different guide RNA scoring functions in one simple graphical interface. It allows investigators to simultaneously visualize and sort through every guide targeting the protein-coding regions of any mouse or human gene. RESULTS Utilizing a multidimensional graphical display featuring two plots and four axes, Guide Picker can analyze all guides while filtering based on four different criteria at a time. Guide Picker further facilitates the CRISPR design process by using pre-computed scores for all guides, thereby offering rapid guide RNA generation and selection. CONCLUSIONS The ease-of-use of Guide Picker complements CRISPR itself, matching a powerful and modular biological system with a flexible online web tool that can be used in a variety of genome editing experimental contexts.
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Affiliation(s)
- Soren H. Hough
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | - Kris Kancleris
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | - Leigh Brody
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | | | - Joseph Wolanski
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | - Keith Dunaway
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | | | - Victor Dillard
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
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Dunaway K, Goorha S, Matelski L, Urraca N, Lein PJ, Korf I, Reiter LT, LaSalle JM. Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns. Stem Cells 2017; 35:981-988. [PMID: 28032673 DOI: 10.1002/stem.2563] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/27/2016] [Accepted: 12/12/2016] [Indexed: 12/20/2022]
Abstract
Early embryonic stages of pluripotency are modeled for epigenomic studies primarily with human embryonic stem cells (ESC) or induced pluripotent stem cells (iPSCs). For analysis of DNA methylation however, ESCs and iPSCs do not accurately reflect the DNA methylation levels found in preimplantation embryos. Whole genome bisulfite sequencing (WGBS) approaches have revealed the presence of large partially methylated domains (PMDs) covering 30%-40% of the genome in oocytes, preimplantation embryos, and placenta. In contrast, ESCs and iPSCs show abnormally high levels of DNA methylation compared to inner cell mass (ICM) or placenta. Here we show that dental pulp stem cells (DPSCs), derived from baby teeth and cultured in serum-containing media, have PMDs and mimic the ICM and placental methylome more closely than iPSCs and ESCs. By principal component analysis, DPSC methylation patterns were more similar to two other neural stem cell types of human derivation (EPI-NCSC and LUHMES) and placenta than were iPSCs, ESCs or other human cell lines (SH-SY5Y, B lymphoblast, IMR90). To test the suitability of DPSCs in modeling epigenetic differences associated with disease, we compared methylation patterns of DPSCs derived from children with chromosome 15q11.2-q13.3 maternal duplication (Dup15q) to controls. Differential methylation region (DMR) analyses revealed the expected Dup15q hypermethylation at the imprinting control region, as well as hypomethylation over SNORD116, and novel DMRs over 147 genes, including several autism candidate genes. Together these data suggest that DPSCs are a useful model for epigenomic and functional studies of human neurodevelopmental disorders. Stem Cells 2017;35:981-988.
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Affiliation(s)
- Keith Dunaway
- Medical Microbiology and Immunology, UC Davis, Davis, California, USA.,Genome Center, UC Davis, Davis, California, USA.,MIND Institute, UC Davis, Davis, California, USA.,Center for Children's Environmental Health, UC Davis, Davis, California, USA
| | - Sarita Goorha
- Department of Neurology, UTHSC, Memphis, Tennessee, USA.,Department of Pediatrics, UTHSC, Memphis, Tennessee, USA.,Department of Anatomy and Neurobiology, UTHSC, Memphis, Tennessee, USA
| | - Lauren Matelski
- MIND Institute, UC Davis, Davis, California, USA.,Center for Children's Environmental Health, UC Davis, Davis, California, USA.,Internal Medicine, UC Davis, Davis, California, USA
| | - Nora Urraca
- Department of Neurology, UTHSC, Memphis, Tennessee, USA
| | - Pamela J Lein
- MIND Institute, UC Davis, Davis, California, USA.,Center for Children's Environmental Health, UC Davis, Davis, California, USA.,Molecular Biosciences, UC Davis, Davis, California, USA
| | - Ian Korf
- Genome Center, UC Davis, Davis, California, USA.,Molecular and Cellular Biology, UC Davis, Davis, California, USA
| | - Lawrence T Reiter
- Department of Neurology, UTHSC, Memphis, Tennessee, USA.,Department of Pediatrics, UTHSC, Memphis, Tennessee, USA.,Department of Anatomy and Neurobiology, UTHSC, Memphis, Tennessee, USA
| | - Janine M LaSalle
- Medical Microbiology and Immunology, UC Davis, Davis, California, USA.,Genome Center, UC Davis, Davis, California, USA.,MIND Institute, UC Davis, Davis, California, USA.,Center for Children's Environmental Health, UC Davis, Davis, California, USA
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Lee W, Yun JM, Woods R, Dunaway K, Yasui DH, Lasalle JM, Gong Q. MeCP2 regulates activity-dependent transcriptional responses in olfactory sensory neurons. Hum Mol Genet 2014; 23:6366-74. [PMID: 25008110 DOI: 10.1093/hmg/ddu358] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
During postnatal development, neuronal activity controls the remodeling of initially imprecise neuronal connections through the regulation of gene expression. MeCP2 binds to methylated DNA and modulates gene expression during neuronal development and MECP2 mutation causes the autistic disorder Rett syndrome. To investigate a role for MeCP2 in neuronal circuit refinement and to identify activity-dependent MeCP2 transcription regulations, we leveraged the precise organization and accessibility of olfactory sensory axons to manipulation of neuronal activity through odorant exposure in vivo. We demonstrate that olfactory sensory axons failed to develop complete convergence when Mecp2 is deficient in olfactory sensory neurons (OSNs) in an otherwise wild-type animal. Furthermore, we demonstrate that expression of selected adhesion genes was elevated in Mecp2-deficient glomeruli, while acute odor stimulation in control mice resulted in significantly reduced MeCP2 binding to these gene loci, correlating with increased expression. Thus, MeCP2 is required for both circuitry refinement and activity-dependent transcriptional responses in OSNs.
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Affiliation(s)
- Wooje Lee
- Department of Cell Biology and Human Anatomy
| | - Jung-Mi Yun
- Department of Food and Nutrition, Kwangju Women's University, Gwang ju 506-713, South Korea and
| | - Rima Woods
- Department of Medical Microbiology and Immunology
| | | | - Dag H Yasui
- Department of Medical Microbiology and Immunology
| | - Janine M Lasalle
- Department of Medical Microbiology and Immunology, UC Davis Genome Center, University of California at Davis, School of Medicine, Davis, CA 95616, USA, UC Davis MIND Institute, Sacramento, CA 95817, USA
| | - Qizhi Gong
- Department of Cell Biology and Human Anatomy,
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Singleton MK, Gonzales ML, Leung KN, Yasui DH, Schroeder DI, Dunaway K, LaSalle JM. MeCP2 is required for global heterochromatic and nucleolar changes during activity-dependent neuronal maturation. Neurobiol Dis 2011; 43:190-200. [PMID: 21420494 DOI: 10.1016/j.nbd.2011.03.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 01/24/2011] [Accepted: 03/11/2011] [Indexed: 10/18/2022] Open
Abstract
Mutations in MECP2, encoding methyl CpG binding protein 2, cause the neurodevelopmental disorder Rett syndrome. MeCP2 is an abundant nuclear protein that binds to chromatin and modulates transcription in response to neuronal activity. Prior studies of MeCP2 function have focused on specific gene targets of MeCP2, but a more global role for MeCP2 in neuronal nuclear maturation has remained unexplored. MeCP2 levels increase during postnatal brain development, coinciding with dynamic changes in neuronal chromatin architecture, particularly detectable as changes in size, number, and location of nucleoli and perinucleolar heterochromatic chromocenters. To determine a potential role for MeCP2 in neuronal chromatin maturational changes, we measured nucleoli and chromocenters in developing wild-type and Mecp2-deficient mouse cortical sections, as well as mouse primary cortical neurons and a human neuronal cell line following induced maturation. Mecp2-deficient mouse neurons exhibited significant differences in nucleolar and chromocenter number and size, as more abundant, smaller nucleoli in brain and primary neurons compared to wild-type, consistent with delayed neuronal nuclear maturation in the absence of MeCP2. Primary neurons increased chromocenter size following depolarization in wild-type, but not Mecp2-deficient cultures. Wild-type MECP2e1 over-expression in human SH-SY5Y cells was sufficient to induce significantly larger nucleoli, but not a T158M mutation of the methyl-binding domain. These results suggest that, in addition to the established role of MeCP2 in transcriptional regulation of specific target genes, the global chromatin-binding function of MeCP2 is essential for activity-dependent global chromatin dynamics during postnatal neuronal maturation.
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Affiliation(s)
- Malaika K Singleton
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, and MIND Institute, University of California, Davis, CA 95616, USA
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