1
|
Zimmer C, Hanson HE, Garrison M, Reese D, Dor R, Søraker JS, Ho Thu P, Sheldon EL, Martin LB. Immune gene expression and epigenetic potential affect the consumption of risky food by female house sparrows. Brain Behav Immun 2024; 119:6-13. [PMID: 38552921 DOI: 10.1016/j.bbi.2024.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 06/11/2024] Open
Abstract
When organisms move into new areas, they are likely to encounter novel food resources. Even if they are nutritious, these foods can also be risky, as they might be contaminated by parasites. The behavioural immune system of animals could help them avoid the negative effects of contaminated resources, but our understanding of behavioural immunity is limited, particularly whether and how behavioural immunity interacts with physiological immunity. Here, we asked about the potential for interplay between these two traits, specifically how the propensity of an individual house sparrow (Passer domesticus) to take foraging risks was related to its ability to regulate a key facet of its immune response to bacterial pathogens. Previously, we found that sparrows at expanding geographic range edges were more exploratory and less risk-averse to novel foods; in those same populations, birds tended to over-express Toll-like receptor 4 (TLR4), a pattern-recognition receptor that distinguishes cell-wall components of Gram-negative bacteria, making it the major sensor of potentially lethal gut microbial infections including salmonellosis. When we investigated how birds would respond to a typical diet (i.e., mixed seeds) spiked with domesticated chicken faeces, birds that expressed more TLR4 or had higher epigenetic potential for TLR4 (more CpG dinucleotides in the putative gene promoter) ate more food, spiked or not. Females expressing abundant TLR4 were also willing to take more foraging risks and ate more spiked food. In males, TLR4 expression was not associated with risk-taking. Altogether, our results indicate that behaviour and immunity covary among individual house sparrows, particularly in females where those birds that maintain more immune surveillance also are more disposed to take foraging risks.
Collapse
Affiliation(s)
- Cedric Zimmer
- Global Health and Interdisciplinary Disease Research Center, University of South Florida 33612, USA; Laboratoire d'Ethologie Expérimentale et Comparée, LEEC, Université Sorbonne Paris Nord, UR 4443, 93430 Villetaneuse, France.
| | - Haley E Hanson
- Global Health and Interdisciplinary Disease Research Center, University of South Florida 33612, USA
| | - Marisa Garrison
- Global Health and Interdisciplinary Disease Research Center, University of South Florida 33612, USA
| | - Darrys Reese
- Global Health and Interdisciplinary Disease Research Center, University of South Florida 33612, USA
| | - Roi Dor
- Department of Natural Life Sciences, The Open University of Israel, Ra'Anana, Israel
| | - Jørgen S Søraker
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology Høgskoleringen 5, NO-7491 Trondheim, Norway; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Phuong Ho Thu
- Vietnam National University of Forestry, Hanoi 100000, Viet Nam
| | - Elizabeth L Sheldon
- Global Health and Interdisciplinary Disease Research Center, University of South Florida 33612, USA
| | - Lynn B Martin
- Global Health and Interdisciplinary Disease Research Center, University of South Florida 33612, USA
| |
Collapse
|
2
|
Creasey LD, Tauber E. Interconnected Codons: Unravelling the Epigenetic Significance of Flanking Sequences in CpG Dyads. J Mol Evol 2024; 92:207-216. [PMID: 38634873 PMCID: PMC11169003 DOI: 10.1007/s00239-024-10172-1] [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: 10/17/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Hypothesizing that CpG codon dyads, formed by consecutive codons containing a cytosine-guanine pair (NNC-GNN), may play a crucial role in gene function, we conducted an extensive analysis to investigate their distribution and conservation within mammalian genes. Our findings reveal that genes characterized by a high density of CpG codon dyads are notably associated with homeobox domains and RNA polymerase II transcription factors. Conversely, genes exhibiting low CpG codon dyad density have links to DNA damage repair and mitosis. Importantly, our study identifies a re-markable increase in expressed genes that harbor CpG during embryonic development, suggesting their potential involvement in gene regulation at these developmental stages. These results under-score the functional significance of CpG codon dyads in DNA methylation and gene expression, fur-ther demonstrating the coevolution of consecutive codons and their contribution to codon usage bias.
Collapse
Affiliation(s)
- Leo Douglas Creasey
- Department of Evolutionary and Environmental Biology, and Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Haifa, 3498838, Israel
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, and Institute of Evolution, University of Haifa, 199 Abba-Hushi Avenue, Haifa, 3498838, Israel.
| |
Collapse
|
3
|
Tompkins JD. Transgenerational Epigenetic DNA Methylation Editing and Human Disease. Biomolecules 2023; 13:1684. [PMID: 38136557 PMCID: PMC10742326 DOI: 10.3390/biom13121684] [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: 11/01/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
During gestation, maternal (F0), embryonic (F1), and migrating primordial germ cell (F2) genomes can be simultaneously exposed to environmental influences. Accumulating evidence suggests that operating epi- or above the genetic DNA sequence, covalent DNA methylation (DNAme) can be recorded onto DNA in response to environmental insults, some sites which escape normal germline erasure. These appear to intrinsically regulate future disease propensity, even transgenerationally. Thus, an organism's genome can undergo epigenetic adjustment based on environmental influences experienced by prior generations. During the earliest stages of mammalian development, the three-dimensional presentation of the genome is dramatically changed, and DNAme is removed genome wide. Why, then, do some pathological DNAme patterns appear to be heritable? Are these correctable? In the following sections, I review concepts of transgenerational epigenetics and recent work towards programming transgenerational DNAme. A framework for editing heritable DNAme and challenges are discussed, and ethics in human research is introduced.
Collapse
Affiliation(s)
- Joshua D Tompkins
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| |
Collapse
|
4
|
Ratiometric Electrochemical Biosensing of Methyltransferase Activity. Catalysts 2022. [DOI: 10.3390/catal12111362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, a novel ratiometric electrochemical readout platform was proposed and developed for the fast and flexible analysis of M.SssI methyltransferase (MTase) activity. In this platform, two hairpin DNAs (H1 and H2) were designed. H1 contains the palindromic sequence of 5′-CCGG-3′ in its stem which could be methylated and hybridize with H2 labeled by methylene blue (MB) as one of the signal reporters on a gold electrode (GE) in the presence of M.SssI MTase. Additionally, a specific immunoreaction was introduced by conjugating an anti-5-methylcytosine antibody, a DNA CpG methylation recognition unit, with 1,3-ferrocenedicarboxylic acid (Fc) as the second signal reporter. The results showed that when the Fc tag approaches, the MB tag was far from the gold electrode surface, resulting in a decrease in the oxidation peak current of MB (IMB) and an increase in the oxidation peak current of Fc (IFc). The ratiometric electrochemical method above shows the linear range of detection was 0 U/mL 40 U/mL with a detection limit of 0.083 U/mL (the mean signal of blank measures þ3s).
Collapse
|
5
|
The Mutagenic Consequences of DNA Methylation within and across Generations. EPIGENOMES 2022; 6:epigenomes6040033. [PMID: 36278679 PMCID: PMC9624357 DOI: 10.3390/epigenomes6040033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is an epigenetic modification with wide-ranging consequences across the life of an organism. This modification can be stable, persisting through development despite changing environmental conditions. However, in other contexts, DNA methylation can also be flexible, underlying organismal phenotypic plasticity. One underappreciated aspect of DNA methylation is that it is a potent mutagen; methylated cytosines mutate at a much faster rate than other genetic motifs. This mutagenic property of DNA methylation has been largely ignored in eco-evolutionary literature, despite its prevalence. Here, we explore how DNA methylation induced by environmental and other factors could promote mutation and lead to evolutionary change at a more rapid rate and in a more directed manner than through stochastic genetic mutations alone. We argue for future research on the evolutionary implications of DNA methylation driven mutations both within the lifetime of organisms, as well as across timescales.
Collapse
|
6
|
Hanson HE, Wang C, Schrey AW, Liebl AL, Ravinet M, Jiang RH, Martin LB. Epigenetic Potential and DNA Methylation in an Ongoing House Sparrow (Passer domesticus) Range Expansion. Am Nat 2022; 200:662-674. [DOI: 10.1086/720950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
7
|
Al Adhami H, Bardet AF, Dumas M, Cleroux E, Guibert S, Fauque P, Acloque H, Weber M. A comparative methylome analysis reveals conservation and divergence of DNA methylation patterns and functions in vertebrates. BMC Biol 2022; 20:70. [PMID: 35317801 PMCID: PMC8941758 DOI: 10.1186/s12915-022-01270-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/04/2022] [Indexed: 12/24/2022] Open
Abstract
Background Cytosine DNA methylation is a heritable epigenetic mark present in most eukaryotic groups. While the patterns and functions of DNA methylation have been extensively studied in mouse and human, their conservation in other vertebrates remains poorly explored. In this study, we interrogated the distribution and function of DNA methylation in primary fibroblasts of seven vertebrate species including bio-medical models and livestock species (human, mouse, rabbit, dog, cow, pig, and chicken). Results Our data highlight both divergence and conservation of DNA methylation patterns and functions. We show that the chicken genome is hypomethylated compared to other vertebrates. Furthermore, compared to mouse, other species show a higher frequency of methylation of CpG-rich DNA. We reveal the conservation of large unmethylated valleys and patterns of DNA methylation associated with X-chromosome inactivation through vertebrate evolution and make predictions of conserved sets of imprinted genes across mammals. Finally, using chemical inhibition of DNA methylation, we show that the silencing of germline genes and endogenous retroviruses (ERVs) are conserved functions of DNA methylation in vertebrates. Conclusions Our data highlight conserved properties of DNA methylation in vertebrate genomes but at the same time point to differences between mouse and other vertebrate species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01270-x.
Collapse
Affiliation(s)
- Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Anaïs Flore Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Elouan Cleroux
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Sylvain Guibert
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Patricia Fauque
- Université Bourgogne Franche-Comté, Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, 2 Rue Angélique Ducoudray, 21000, Dijon, France.,CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction - CECOS, 14 rue Gaffarel, 21000, Dijon, France
| | - Hervé Acloque
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Michael Weber
- University of Strasbourg, Strasbourg, France. .,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France.
| |
Collapse
|
8
|
Garcia P, Fernandez-Hernandez R, Cuadrado A, Coca I, Gomez A, Maqueda M, Latorre-Pellicer A, Puisac B, Ramos FJ, Sandoval J, Esteller M, Mosquera JL, Rodriguez J, Pié J, Losada A, Queralt E. Disruption of NIPBL/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome. Nat Commun 2021; 12:4551. [PMID: 34315879 PMCID: PMC8316422 DOI: 10.1038/s41467-021-24808-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/05/2021] [Indexed: 12/31/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare disease affecting multiple organs and systems during development. Mutations in the cohesin loader, NIPBL/Scc2, were first described and are the most frequent in clinically diagnosed CdLS patients. The molecular mechanisms driving CdLS phenotypes are not understood. In addition to its canonical role in sister chromatid cohesion, cohesin is implicated in the spatial organization of the genome. Here, we investigate the transcriptome of CdLS patient-derived primary fibroblasts and observe the downregulation of genes involved in development and system skeletal organization, providing a link to the developmental alterations and limb abnormalities characteristic of CdLS patients. Genome-wide distribution studies demonstrate a global reduction of NIPBL at the NIPBL-associated high GC content regions in CdLS-derived cells. In addition, cohesin accumulates at NIPBL-occupied sites at CpG islands potentially due to reduced cohesin translocation along chromosomes, and fewer cohesin peaks colocalize with CTCF.
Collapse
Affiliation(s)
- Patricia Garcia
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.
| | - Rita Fernandez-Hernandez
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Cuadrado
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ignacio Coca
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Grup de Recerca de Reumatologia, Parc Científic de Barcelona, Barcelona, Spain
| | - Maria Maqueda
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Feliciano J Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit (UByMP) and Epigenomics Core Facility, Health Research Institute La Fe (IISLaFe), Valencia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Jose Luis Mosquera
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Jairo Rodriguez
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - J Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ethel Queralt
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.
| |
Collapse
|
9
|
Hanson HE, Zimmer C, Koussayer B, Schrey AW, Maddox JD, Martin LB. Epigenetic potential affects immune gene expression in house sparrows. J Exp Biol 2021; 224:224/6/jeb238451. [PMID: 33775934 DOI: 10.1242/jeb.238451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetic mechanisms may play a central role in mediating phenotypic plasticity, especially during range expansions, when populations face a suite of novel environmental conditions. Individuals may differ in their epigenetic potential (EP; their capacity for epigenetic modifications of gene expression), which may affect their ability to colonize new areas. One form of EP, the number of CpG sites, is higher in introduced house sparrows (Passer domesticus) than in native birds in the promoter region of a microbial surveillance gene, Toll-like Receptor 4 (TLR4), which may allow invading birds to fine-tune their immune responses to unfamiliar parasites. Here, we compared TLR4 gene expression from whole blood, liver and spleen in house sparrows with different EP, first challenging some birds with lipopolysaccharide (LPS), to increase gene expression by simulating a natural infection. We expected that high EP would predict high inducibility and reversibility of TLR4 expression in the blood of birds treated with LPS, but we did not make directional predictions regarding organs, as we could not repeatedly sample these tissues. We found that EP was predictive of TLR4 expression in all tissues. Birds with high EP expressed more TLR4 in the blood than individuals with low EP, regardless of treatment with LPS. Only females with high EP exhibited reversibility in gene expression. Further, the effect of EP varied between sexes and among tissues. Together, these data support EP as one regulator of TLR4 expression.
Collapse
Affiliation(s)
- Haley E Hanson
- University of South Florida, Global Health and Infectious Disease Research, Tampa, FL 33612, USA
| | - Cedric Zimmer
- University of South Florida, Global Health and Infectious Disease Research, Tampa, FL 33612, USA
| | - Bilal Koussayer
- University of South Florida, Global Health and Infectious Disease Research, Tampa, FL 33612, USA
| | - Aaron W Schrey
- Georgia Southern University Armstrong Campus, Department of Biology, Savannah, GA 31419, USA
| | - J Dylan Maddox
- Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.,American Public University System, Environmental Sciences, Charles Town, WV 25414, USA.,Universidad Científica del Perú, Laboratorio de Biotecnología y Bioenergética, Iquitos 16007, Perú
| | - Lynn B Martin
- University of South Florida, Global Health and Infectious Disease Research, Tampa, FL 33612, USA
| |
Collapse
|
10
|
Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194567. [PMID: 32360393 PMCID: PMC7294231 DOI: 10.1016/j.bbagrm.2020.194567] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. However, approximately 70% of vertebrate gene promoters are associated with DNA elements called CpG islands (CGIs) that are refractory to DNA methylation. CGIs integrate the activity of a range of chromatin-regulating factors that can post-translationally modify histones and modulate gene expression. This is exemplified by the trimethylation of histone H3 at lysine 4 (H3K4me3), which is enriched at CGI-associated gene promoters and correlates with transcriptional activity. Through studying H3K4me3 at CGIs it has become clear that CGIs shape the distribution of H3K4me3 and, in turn, H3K4me3 influences the chromatin landscape at CGIs. Here we will discuss our understanding of the emerging relationship between CGIs, H3K4me3, and gene expression.
Collapse
|
11
|
Hanson HE, Koussayer B, Kilvitis HJ, Schrey AW, Maddox JD, Martin LB. Epigenetic Potential in Native and Introduced Populations of House Sparrows (Passer domesticus). Integr Comp Biol 2020; 60:1458-1468. [PMID: 32497186 DOI: 10.1093/icb/icaa060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Epigenetic potential, defined as the capacity for epigenetically-mediated phenotypic plasticity, may play an important role during range expansions. During range expansions, populations may encounter relatively novel challenges while experiencing lower genetic diversity. Phenotypic plasticity via epigenetic potential might be selectively advantageous at the time of initial introduction or during spread into new areas, enabling introduced organisms to cope rapidly with novel challenges. Here, we asked whether one form of epigenetic potential (i.e., the abundance of CpG sites) in three microbial surveillance genes: Toll-like receptors (TLRs) 1B (TLR1B), 2A (TLR2A), and 4 (TLR4) varied between native and introduced house sparrows (Passer domesticus). Using an opportunistic approach based on samples collected from sparrow populations around the world, we found that introduced birds had more CpG sites in TLR2A and TLR4, but not TLR1B, than native ones. Introduced birds also lost more CpG sites in TLR1B, gained more CpG sites in TLR2A, and lost fewer CpG sites in TLR4 compared to native birds. These results were not driven by differences in genetic diversity or population genetic structure, and many CpG sites fell within predicted transcription factor binding sites (TFBS), with losses and gains of CpG sites altering predicted TFBS. Although we lacked statistical power to conduct the most rigorous possible analyses, these results suggest that epigenetic potential may play a role in house sparrow range expansions, but additional work will be critical to elucidating how epigenetic potential affects gene expression and hence phenotypic plasticity at the individual, population, and species levels.
Collapse
Affiliation(s)
- Haley E Hanson
- Global and Planetary Health, University of South Florida, 3720 Spectrum Blvd, Suite 304, Tampa, FL 33620, USA
| | - Bilal Koussayer
- Global and Planetary Health, University of South Florida, 3720 Spectrum Blvd, Suite 304, Tampa, FL 33620, USA
| | - Holly J Kilvitis
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Ave, SCA110, Tampa, FL 33620, USA
| | - Aaron W Schrey
- Department of Biology, Georgia Southern University, Armstrong Campus, 11935 Abercorn St, SC1010, Savannah, GA 31419, USA
| | - J Dylan Maddox
- Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.,Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú, Iquitos, Perú.,American Public University System, Environmental Sciences, Charles Town, WV 25414, USA
| | - Lynn B Martin
- Global and Planetary Health, University of South Florida, 3720 Spectrum Blvd, Suite 304, Tampa, FL 33620, USA
| |
Collapse
|
12
|
Niu L, Wang X, Mao G, Li Z, Ji X, He Z. Sensitive fluorescent detection of methyltransferase based on thermosensitive poly(N-isopropylacrylamide). Talanta 2018; 189:579-584. [PMID: 30086963 DOI: 10.1016/j.talanta.2018.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 12/21/2022]
Abstract
DNA methyltransferase (MTase) has a crucial role in many biological processes, its abnormal expression level has been regarded as a predictive cancer biomarker. Herein, a sensitive fluorescence method based on thermosensitive poly (N-isopr-opylacrylamide) was developed to assay of M.SssI activity. When the M.SssI was introduced, dsDNA was methylated at palindromic sequence 5'-CmCGG-3' and became resistant to cleavage by the endonuclease HpaII. Therefore, a biotin modified ssDNA and a FAM modified ssDNA were designed including the recognized sites for both methyltransferase M.SssI and endonuclease HpaII. By SA-biotin intereaction, the DNA was conjugated to thermosensitive poly (N-isopropylacrylamide) modified by SA, the methylated substrate fluorescence was increased with the concentration of M.SssI increasing. The proposed method has a low detection limit of 0.18 U/mL. This simple method can be a useful tool to apply in diagnosis and biomedical research, which was successfully investigated in the serum sample.
Collapse
Affiliation(s)
- Longqing Niu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xinxin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Guobin Mao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zheng Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xinghu Ji
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhike He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| |
Collapse
|
13
|
Pranckėnienė L, Jakaitienė A, Ambrozaitytė L, Kavaliauskienė I, Kučinskas V. Insights Into de novo Mutation Variation in Lithuanian Exome. Front Genet 2018; 9:315. [PMID: 30154829 PMCID: PMC6102505 DOI: 10.3389/fgene.2018.00315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/24/2018] [Indexed: 01/23/2023] Open
Abstract
In the last decade, one of the biggest challenges in genomics research has been to distinguish definitive pathogenic variants from all likely pathogenic variants identified by next-generation sequencing. This task is particularly complex because of our lack of knowledge regarding overall genome variation and pathogenicity of the variants. Therefore, obtaining sufficient information about genome variants in the general population is necessary as such data could be used for the interpretation of de novo mutations (DNMs) in the context of patient's phenotype in cases of sporadic genetic disease. In this study, data from whole-exome sequencing of the general population in Lithuania were directly examined. In total, 84 (VarScan) and 95 (VarSeqTM) DNMs were identified and validated using different algorithms. Thirty-nine of these mutations were considered likely to be pathogenic based on gene function, evolutionary conservation, and mutation impact. The mutation rate estimated per position pair per generation was 2.74 × 10-8 [95% CI: 2.24 × 10-8-3.35 × 10-8] (VarScan) and 2.4 × 10-8 [95% CI: 1.96 × 10-8-2.99 × 10-8] (VarSeqTM), with 1.77 × 10-8 [95% CI: 6.03 × 10-9-5.2 × 10-8] de novo indels per position per generation. The rate of germline DNMs in the Lithuanian population and the effects of the genomic and epigenetic context on DNM formation were calculated for the first time in this study, providing a basis for further analysis of DNMs in individuals with genetic diseases. Considering these findings, additional studies in patient groups with genetic diseases with unclear etiology may facilitate our ability to distinguish certain pathogenic or adaptive DNMs from tolerated background DNMs and to reliably identify disease-causing DNMs by their properties through direct observation.
Collapse
Affiliation(s)
- Laura Pranckėnienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | | | | | | | | |
Collapse
|
14
|
Weinhouse C, Truong L, Meyer JN, Allard P. Caenorhabditis elegans as an emerging model system in environmental epigenetics. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:560-575. [PMID: 30091255 PMCID: PMC6113102 DOI: 10.1002/em.22203] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/13/2018] [Accepted: 04/19/2018] [Indexed: 05/19/2023]
Abstract
The roundworm Caenorhabitis elegans has been an established model organism for the study of genetics and developmental biology, including studies of transcriptional regulation, since the 1970s. This model organism has continued to be used as a classical model system as the field of transcriptional regulation has expanded to include scientific advances in epigenetics and chromatin biology. In the last several decades, C. elegans has emerged as a powerful model for environmental toxicology, particularly for the study of chemical genotoxicity. Here, we outline the utility and applicability of C. elegans as a powerful model organism for mechanistic studies of environmental influences on the epigenome. Our goal in this article is to inform the field of environmental epigenetics of the strengths and limitations of the well-established C. elegans model organism as an emerging model for medium-throughput, in vivo exploration of the role of exogenous chemical stimuli in transcriptional regulation, developmental epigenetic reprogramming, and epigenetic memory and inheritance. As the field of environmental epigenetics matures, and research begins to map mechanisms underlying observed associations, new toolkits and model systems, particularly manipulable, scalable in vivo systems that accurately model human transcriptional regulatory circuits, will provide an essential experimental bridge between in vitro biochemical experiments and mammalian model systems. Environ. Mol. Mutagen. 59:560-575, 2018. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Caren Weinhouse
- Duke Global Health Institute, Duke University, Durham, North Carolina
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Lisa Truong
- UCLA Human Genetics and Genomic Analysis Training Program, University of California, Los Angeles; Los Angeles, California
| | - Joel N. Meyer
- Duke Global Health Institute, Duke University, Durham, North Carolina
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Patrick Allard
- Institute for Society and Genetics, University of California at Los Angeles, Los Angeles, California
| |
Collapse
|
15
|
Li Y, Zheng H, Wang Q, Zhou C, Wei L, Liu X, Zhang W, Zhang Y, Du Z, Wang X, Xie W. Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys. Genome Biol 2018; 19:18. [PMID: 29422066 PMCID: PMC5806489 DOI: 10.1186/s13059-018-1390-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/10/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Previous studies showed that the majority of developmental genes are devoid of DNA methylation at promoters even when they are repressed. Such hypomethylated regions at developmental genes are unusually large and extend well beyond proximal promoters, forming DNA methylation valleys (DMVs) or DNA methylation canyons. However, it remains elusive how most developmental genes can evade DNA methylation regardless of their transcriptional states. RESULTS We show that DMVs are hypomethylated in development and are highly conserved across vertebrates. Importantly, DMVs are hotspots of regulatory regions for key developmental genes and show low levels of deamination mutation rates. By analyzing a panel of DNA methylomes from mouse tissues, we identify a subset of DMVs that are dynamically methylated. These DMVs are strongly enriched for Polycomb-deposited H3K27me3 when the associated genes are silenced, and surprisingly show elevated DNA methylation upon gene activation. 4C-seq analyses indicates that Polycomb-bound DMVs form insulated and self-interacting chromatin domains. Further investigations show that DNA hypomethylation is better correlated with the binding of Polycomb than with H3K27me3. In support of a role of Polycomb in DMV hypomethylation, we observe aberrant methylation in DMVs in mouse embryonic stem cells deficient in the EED protein. Finally, we show that Polycomb regulates hypomethylation of DMVs likely through ten-eleven translocation (TET) proteins. CONCLUSIONS We show that Polycomb promotes the hypomethylation of DMVs near key developmental genes. These data reveal a delicate interplay between histone modifiers and DNA methylation, which contributes to their division at distinct gene targets, allowing lineage-specifying genes to largely maintain DNA methylation-free at regulatory elements.
Collapse
Affiliation(s)
- Yuanyuan Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hui Zheng
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chen Zhou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lei Wei
- Bioinformatics Division, TNLIST/MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Xuehui Liu
- Bioinformatics Division, TNLIST/MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Wenhao Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaowo Wang
- Bioinformatics Division, TNLIST/MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
16
|
Wang ZY, Wang LJ, Zhang Q, Tang B, Zhang CY. Single quantum dot-based nanosensor for sensitive detection of 5-methylcytosine at both CpG and non-CpG sites. Chem Sci 2018; 9:1330-1338. [PMID: 29675180 PMCID: PMC5887231 DOI: 10.1039/c7sc04813k] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/12/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an important epigenetic modification in human genomes. Herein, we develop a single quantum dot (QD)-based nanosensor for sensitive detection of DNA methylation at both CpG and non-CpG sites using tricyclic ligation chain reaction (LCR)-mediated QD-based fluorescence resonance energy transfer (FRET). We design two sets of DNA probes (X and Y, X' and Y') for methylated DNA assay. In the presence of thermostable DNA ligase, probes X and Y may adjacently hybridize with the methylated DNA to obtain the ligated XY products which may function as the templates for probes X' and Y' to generate the X'Y' products. The resultant X'Y' products may in turn act as the templates to ligate probes X and Y for the generation of XY products, consequently inducing tricyclic LCR amplification under thermal denaturation conditions to generate a large number of XY products. The subsequent hybridization of XY products with the capture and reporter probes results in the formation of sandwich hybrids which may assemble on the 605QD surface to obtain 605QD-oligonucleotide-Cy5 nanostructures, inducing efficient FRET from the 605QD to Cy5 and the emission of Cy5. This nanosensor can detect DNA methylation at single 5-methylcytosine (5-mC) resolution with a detection limit of as low as 1.0 aM and a large dynamic range of 7 orders of magnitude. Moreover, this nanosensor can distinguish as low as a 0.01% methylation level, and it can detect DNA methylation in human lung cancer cells as well, holding great potential for accurate epigenetic evaluation and early cancer diagnosis.
Collapse
Affiliation(s)
- Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; ; Tel: +86-0531-86186033
| | - Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; ; Tel: +86-0531-86186033
| | - Qianyi Zhang
- Nantou High School Shenzhen , Shenzhen , 518052 , China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; ; Tel: +86-0531-86186033
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; ; Tel: +86-0531-86186033
| |
Collapse
|
17
|
Yang Y, Yang G, Chen H, Zhang H, Feng JJ, Cai C. Electrochemical signal-amplified detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA using glucose modification coupled with restriction endonucleases. Analyst 2018; 143:2051-2056. [DOI: 10.1039/c7an02049j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A sensitive electrochemical assay based on glucose modification coupled with restriction endonucleases was fabricated for the detection of 5-methylcytosine and 5-hydroxymethylcytosine in DNA.
Collapse
Affiliation(s)
- Yin Yang
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Guoqing Yang
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Hongfei Chen
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Hui Zhang
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| | - Jiu-Ju Feng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials
- College of Chemistry and Life Sciences
- Zhejiang Normal University
- Jinhua 321004
- China
| | - Chenxin Cai
- Jiangsu Key Laboratory of Biomedical Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- National and Local Joint Engineering Research Center of Biomedical Functional Materials
- Jiangsu Key Laboratory of New Power Batteries
- College of Chemistry and Materials Science
| |
Collapse
|
18
|
Abstract
Background The studies on CpG islands (CGI) and Alu elements functions, evolution, and distribution in the genome started since the discovery in nineteen eighties (1981, 1986, correspondingly). Their highly skewed genome wide distribution implies the non-random retrotransposition pattern. Besides CGIs in gene promoters, CGIs clusters were observed in the homeobox gene regions and in the macrosatellites, but the whole picture of their distribution specifics was not grasped. Attempts to identify any causative features upon their (genome wide) distribution, such as the DNA context mediated preferred insertion sites of Alu repeats, have been made to ascribe their clusters location. Methods Recent emergence of high resolution 3D map of human genome allowed segregating the genome into the large scale chromatin domains of naturally observable nuclear subcompartments, or Topologically Associated Domains (TADs), designated by spatial chromatin distribution. We utilized the chromatin map to elucidate relations between large scale chromatin state and CpG rich elements landscape. In the course of analysis it was confirmed that genes, Alu and CGI clusters maintain obvious, albeit different in strength, preference for open chromatin. For the first time it was clearly shown that the clusters density of the Alu and CGIs monotonically depend on the chromatin accessibility rate. In particular, the highest density of these elements is found in A1 euchromatin regions characterized by a high density of small length genes replicating in the early S-phase. It implies that these elements mediate (CGIs) or are a side element (Alus) of chromatin accessibility. Results We elucidated that both methylated and non-methylated CGIs display the affinity to chromatin accessibility. As a part of comparative genomics section, we elucidated that the dog’s genome non-canonical structure, outstanding in mammals for its high CGIs abundance compared to gene number, is explained by the presence of dense tandem CGI extended hotspots (500 kb on average) in subtelomeric and pericentromeric regions with highly skewed CG content, and not by CGIs global distribution pattern shift. Conclusions The study underlines the close association of CG-rich elements distribution with the newly introduced large scale chromatin state map, proposing a refined standpoint on interrelation of aforementioned genome elements and the chromatin state. To our expertise, the TAD-associated partition model employed in the study is likely the most substantial one regarding CpG rich clusters distribution among the whole genome chromatin/isochores maps available. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0864-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vladimir N Babenko
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia. .,Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia.
| | - Irina V Chadaeva
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia
| | - Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia
| |
Collapse
|
19
|
Zhang H, Yang Y, Dong H, Cai C. A superstructure-based electrochemical assay for signal-amplified detection of DNA methyltransferase activity. Biosens Bioelectron 2016; 86:927-932. [DOI: 10.1016/j.bios.2016.07.103] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/11/2016] [Accepted: 07/28/2016] [Indexed: 12/12/2022]
|
20
|
Zhang H, Dong H, Yang G, Chen H, Cai C. Sensitive Electrochemical Detection of Human Methyltransferase Based on a Dual Signal Amplification Strategy Coupling Gold Nanoparticle–DNA Complexes with Ru(III) Redox Recycling. Anal Chem 2016; 88:11108-11114. [DOI: 10.1021/acs.analchem.6b03163] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hui Zhang
- Jiangsu
Key Laboratory of
New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical
Functional Materials, Jiangsu Key Laboratory of Biomedical Materials,
National and Local Joint Engineering Research Center of Biomedical
Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu 210097, P. R. China
| | - Huilei Dong
- Jiangsu
Key Laboratory of
New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical
Functional Materials, Jiangsu Key Laboratory of Biomedical Materials,
National and Local Joint Engineering Research Center of Biomedical
Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu 210097, P. R. China
| | - Guoqing Yang
- Jiangsu
Key Laboratory of
New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical
Functional Materials, Jiangsu Key Laboratory of Biomedical Materials,
National and Local Joint Engineering Research Center of Biomedical
Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu 210097, P. R. China
| | - Hongfei Chen
- Jiangsu
Key Laboratory of
New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical
Functional Materials, Jiangsu Key Laboratory of Biomedical Materials,
National and Local Joint Engineering Research Center of Biomedical
Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu 210097, P. R. China
| | - Chenxin Cai
- Jiangsu
Key Laboratory of
New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical
Functional Materials, Jiangsu Key Laboratory of Biomedical Materials,
National and Local Joint Engineering Research Center of Biomedical
Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu 210097, P. R. China
| |
Collapse
|
21
|
Labib M, Sargent EH, Kelley SO. Electrochemical Methods for the Analysis of Clinically Relevant Biomolecules. Chem Rev 2016; 116:9001-90. [DOI: 10.1021/acs.chemrev.6b00220] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mahmoud Labib
- Department
of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | | | - Shana O. Kelley
- Department
of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| |
Collapse
|
22
|
Min H, Kong KA, Lee JY, Hong CP, Seo SH, Roh TY, Bae SS, Kim MH. CTCF-mediated Chromatin Loop for the Posterior Hoxc Gene Expression in MEF Cells. IUBMB Life 2016; 68:436-44. [PMID: 27080371 DOI: 10.1002/iub.1504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/15/2016] [Accepted: 03/25/2016] [Indexed: 01/06/2023]
Abstract
Modulation of chromatin structure has been proposed as a molecular mechanism underlying the spatiotemporal collinear expression of Hox genes during development. CCCTC-binding factor (CTCF)-mediated chromatin organization is now recognized as a crucial epigenetic mechanism for transcriptional regulation. Thus, we examined whether CTCF-mediated chromosomal conformation is involved in Hoxc gene expression by comparing wild-type mouse embryonic fibroblast (MEF) cells expressing anterior Hoxc genes with Akt1 null MEFs expressing anterior as well as posterior Hoxc genes. We found that CTCF binding between Hoxc11 and -c12 is important for CTCF-mediated chromosomal loop formation and concomitant posterior Hoxc gene expression. Hypomethylation at this site increased CTCF binding and recapitulated the chromosomal conformation and posterior Hoxc gene expression patterns observed in Akt1 null MEFs. From this work we found that CTCF at the C12|11 does not function as a barrier/boundary, instead let the posterior Hoxc genes switch their interaction from inactive centromeric to active telomeric genomic niche, and concomitant posterior Hoxc gene expression. Although it is not clear whether CTCF affects Hoxc gene expression solely through its looping activity, CTCF-mediated chromatin structural modulation could be an another tier of Hox gene regulation during development. © 2016 IUBMB Life, 68(6):436-444, 2016.
Collapse
Affiliation(s)
- Hyehyun Min
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyoung-Ah Kong
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chang-Pyo Hong
- Department of Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Seong-Hye Seo
- Department of Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Sun Sik Bae
- Department of Pharmacology, MRC For Ischemic Tissue Regeneration, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
23
|
Paluch BE, Naqash AR, Brumberger Z, Nemeth MJ, Griffiths EA. Epigenetics: A primer for clinicians. Blood Rev 2016; 30:285-95. [PMID: 26969414 DOI: 10.1016/j.blre.2016.02.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/04/2016] [Accepted: 02/12/2016] [Indexed: 01/08/2023]
Abstract
With recent advances in cellular biology, we now appreciate that modifications to DNA and histones can have a profound impact on transcription and function, even in the absence of changes to DNA sequence. These modifications, now commonly referred to as "epigenetic" alterations, have changed how we understand cell behavior, reprogramming and differentiation and have provided significant insight into the mechanisms underlying carcinogenesis. Epigenetic alterations, to this point, are largely identified by changes in DNA methylation and hydroxymethylation as well as methylation, acetylation, and phosphorylation of histone tails. These modifications enable significant flexibility in gene expression, rather than just turning genes "ON" or "OFF." Herein we describe the epigenetic landscape in the regulation of gene expression with a particular focus on interrogating DNA methylation in myeloid malignancy.
Collapse
Affiliation(s)
- Benjamin E Paluch
- Department of Pharmacology, Center for Pharmacology and Genetics Building (CGP), Roswell Park Cancer Institute (RPCI), Elm and Carlton Street, 14263 Buffalo, NY, USA.
| | - Abdul R Naqash
- Catholic Health, State University of New York at Buffalo (SUNY), 2157 Main Street, 14214 Buffalo, NY, USA.
| | - Zachary Brumberger
- University at Buffalo State University of New York, School of Medicine and Biomedical Sciences, 3435 Main Street, 14260 Buffalo, NY, USA
| | - Michael J Nemeth
- Department of Medicine, RPCI, Elm and Carlton Street, 14263 Buffalo, NY, USA
| | - Elizabeth A Griffiths
- Department of Pharmacology, Center for Pharmacology and Genetics Building (CGP), Roswell Park Cancer Institute (RPCI), Elm and Carlton Street, 14263 Buffalo, NY, USA; Department of Medicine, RPCI, Elm and Carlton Street, 14263 Buffalo, NY, USA; Leukemia Division, RPCI, Elm and Carlton Street, 14263 Buffalo, NY, USA.
| |
Collapse
|
24
|
Tompkins JD, Jung M, Chen CY, Lin Z, Ye J, Godatha S, Lizhar E, Wu X, Hsu D, Couture LA, Riggs AD. Mapping Human Pluripotent-to-Cardiomyocyte Differentiation: Methylomes, Transcriptomes, and Exon DNA Methylation "Memories". EBioMedicine 2016; 4:74-85. [PMID: 26981572 PMCID: PMC4776252 DOI: 10.1016/j.ebiom.2016.01.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 01/05/2016] [Accepted: 01/15/2016] [Indexed: 11/17/2022] Open
Abstract
The directed differentiation of human cardiomyocytes (CMs) from pluripotent cells provides an invaluable model for understanding mechanisms of cell fate determination and offers considerable promise in cardiac regenerative medicine. Here, we utilize a human embryonic stem cell suspension bank, produced according to a good manufacturing practice, to generate CMs using a fully defined and small molecule-based differentiation strategy. Primitive and cardiac mesoderm purification was used to remove non-committing and multi-lineage populations and this significantly aided the identification of key transcription factors, lncRNAs, and essential signaling pathways that define cardiomyogenesis. Global methylation profiles reflect CM development and we report on CM exon DNA methylation "memories" persisting beyond transcription repression and marking the expression history of numerous developmentally regulated genes, especially transcription factors.
Collapse
Key Words
- Cardiomyocytes
- Cardiomyogenesis
- DNA methylation
- Differentiation
- Epigenetic
- Good manufacturing practice, GMP, epigenetic memory, WNT, hedgehog, transforming growth factor, ROR2, PDGFRα, demethylation, TET, TDG, HOX, TBOX
- Human embryonic stem cells
- Long non-coding RNA
- Mesoderm
- Methylome
- Pluripotent
- Transcriptome
- lncRNA
Collapse
Affiliation(s)
- Joshua D. Tompkins
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Marc Jung
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Chang-yi Chen
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Ziguang Lin
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Jingjing Ye
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Swetha Godatha
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Elizabeth Lizhar
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Xiwei Wu
- Biomedical Informatics Core, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - David Hsu
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Larry A. Couture
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Arthur D. Riggs
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| |
Collapse
|
25
|
Bina M, Wyss P. Impact of the MLL1 morphemes on codon utilization and preservation in CpG Islands. Biopolymers 2015; 103:480-90. [PMID: 25991579 DOI: 10.1002/bip.22681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 05/04/2015] [Accepted: 05/13/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| | - Phillip Wyss
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| |
Collapse
|
26
|
Saint-Carlier E, Riviere G. Regulation of Hox orthologues in the oyster Crassostrea gigas evidences a functional role for promoter DNA methylation in an invertebrate. FEBS Lett 2015; 589:1459-66. [PMID: 25943713 DOI: 10.1016/j.febslet.2015.04.043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/11/2015] [Accepted: 04/20/2015] [Indexed: 11/28/2022]
Abstract
DNA methylation within promoter regions (PRDM) controls vertebrate early gene transcription and thereby development, but is neglected outside this group. However, epigenetic features in the oyster Crassostrea gigas suggest functional significance of PDRM in invertebrates. To investigate this, reporter constructs containing in vitro methylated oyster Hox gene promoters were transfected into oyster embryos. The influence of in vivo methylation was studied using bisulfite sequencing and DNA methyltransferase inhibition during development. Our results demonstrate that methylation controls the transcriptional activity of the promoters investigated, unraveling a functional role for PRDM in a lophotrochozoan, an important finding regarding the evolution of epigenetic regulation.
Collapse
Affiliation(s)
- Emma Saint-Carlier
- IBFA, Institute for Fundamental and Applied Biology, University of Caen, Caen, France; UMR BOREA 'Biologie des organismes et écosystèmes aquatiques' Université de Caen Basse-Normandie, CNRS-7208, IRD-207, MNHN, UPMC, UCBN, UAG, F-14032 Caen, France
| | - Guillaume Riviere
- IBFA, Institute for Fundamental and Applied Biology, University of Caen, Caen, France; UMR BOREA 'Biologie des organismes et écosystèmes aquatiques' Université de Caen Basse-Normandie, CNRS-7208, IRD-207, MNHN, UPMC, UCBN, UAG, F-14032 Caen, France.
| |
Collapse
|
27
|
Fluorescence quenching of graphene oxide combined with the site-specific cleavage of restriction endonuclease for deoxyribonucleic acid demethylase activity assay. Anal Chim Acta 2015; 869:74-80. [DOI: 10.1016/j.aca.2015.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/04/2015] [Accepted: 02/10/2015] [Indexed: 11/21/2022]
|
28
|
Marcinkiewicz KM, Gudas LJ. Altered histone mark deposition and DNA methylation at homeobox genes in human oral squamous cell carcinoma. J Cell Physiol 2014; 229:1405-16. [PMID: 24519855 DOI: 10.1002/jcp.24577] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/16/2014] [Indexed: 01/03/2023]
Abstract
We recently reported a role of polycomb repressive complex 2 (PRC2) and PRC2 trimethylation of histone 3 lysine 27 (H3K27me3) in the regulation of homeobox (HOX) (Marcinkiewicz and Gudas, 2013, Exp Cell Res) gene transcript levels in human oral keratinocytes (OKF6-TERT1R) and tongue squamous cell carcinoma (SCC) cells. Here, we assessed both the levels of various histone modifications at a subset of homeobox genes and genome wide DNA methylation patterns in OKF6-TERT1R and SCC-9 cells by using ERRBS (enhanced reduced representation bisulfite sequencing). We detected the H3K9me3 mark at HOXB7, HOXC10, HOXC13, and HOXD8 at levels higher in OKF6-TERT1R than in SCC-9 cells; at IRX1 and SIX2 the H3K9me3 levels were conversely higher in SCC-9 than in OKF6-TERT1R. The H3K79me3 mark was detectable only at IRX1 in OKF6-TERT1R and at IRX4 in SCC-9 cells. The levels of H3K4me3 and H3K36me3 marks correlate with the transcript levels of the assessed homeobox genes in both OKF6-TERT1R and SCC-9. We detected generally lower CpG methylation levels on DNA in SCC-9 cells at annotated genomic regions which were differentially methylated between OKF6-TERT1R and SCC-9 cells; however, some genomic regions, including the HOX gene clusters, showed DNA methylation at higher levels in SCC-9 than OKF6-TERT1R. Thus, both altered histone modification patterns and changes in DNA methylation are associated with dysregulation of homeobox gene expression in human oral cavity SCC cells, and this dysregulation potentially plays a role in the neoplastic phenotype of oral keratinocytes.
Collapse
Affiliation(s)
- Katarzyna M Marcinkiewicz
- Department of Pharmacology, Weill Cornell Medical College and Weill Graduate School of Biomedical Sciences of Cornell University, New York, New York
| | | |
Collapse
|
29
|
Green TJ, Benkendorff K, Robinson N, Raftos D, Speck P. Anti-viral gene induction is absent upon secondary challenge with double-stranded RNA in the Pacific oyster, Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2014; 39:492-497. [PMID: 24945571 DOI: 10.1016/j.fsi.2014.06.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/04/2014] [Accepted: 06/09/2014] [Indexed: 06/03/2023]
Abstract
Oyster farming is one of the most important aquaculture industries in the world. However, its productivity is increasingly limited by viral disease and we do not yet have management practices, such as protective vaccination, that can control these disease outbreaks. Hence, in the current study we investigated the expression of known anti-viral genes in oysters (Crassostrea gigas) in response to primary and secondary encounter with a virus associated molecular pattern (dsRNA), and tested whether a common form of epigenetic gene regulation (DNA methylation) was associated with the expression of these anti-viral genes. Injection of dsRNA into the adductor muscle resulted in the rapid and transient expression of virus recognition receptors (TLR & MDA5), whereas several anti-viral signalling (IRF & SOC-1) and effector (PKR & viperin) genes were still up-regulated at one week post primary challenge (p < 0.05). This primary encounter with dsRNA appeared to deplete the immune system because anti-viral gene induction was absent in the gills when oysters were given a second injection of dsRNA at 1-week post-primary injection. The expression of DNA methylation genes (DNMT1, DNMT3b, TDG, TET2) and DNA methylation profiles up-stream of specific anti-viral genes (STING, SOC-1 & Viperin) did not change in response to dsRNA injection (p > 0.05). These results collectively suggest that C. gigas does not have an enhanced anti-viral gene response (immune-priming) to secondary dsRNA challenge and that the sustained up-regulation of anti-viral signalling and effector genes following primary challenge is unlikely to be associated with upstream DNA methylation levels.
Collapse
Affiliation(s)
- Timothy J Green
- School of Biological Sciences and Australian Seafood Cooperative Research Centre, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia.
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, Southern Cross University, P.O. Box 157, Lismore, NSW 2480, Australia
| | - Nick Robinson
- School of Biological Sciences and Australian Seafood Cooperative Research Centre, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; Nofima, P.O. Box 210, N-1431 Ås, Norway
| | - David Raftos
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Peter Speck
- School of Biological Sciences and Australian Seafood Cooperative Research Centre, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| |
Collapse
|
30
|
Kong KA, Lee JY, Oh JH, Lee Y, Kim MH. Akt1 mediates the posterior Hoxc gene expression through epigenetic modifications in mouse embryonic fibroblasts. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:793-9. [PMID: 24955524 DOI: 10.1016/j.bbagrm.2014.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 05/09/2014] [Accepted: 06/11/2014] [Indexed: 12/20/2022]
Abstract
The evolutionarily conserved Hox genes are organized in clusters and expressed colinearly to specify body patterning during embryonic development. Previously, Akt1 has been identified as a putative Hox gene regulator through in silico analysis. Substantial upregulation of consecutive 5' Hoxc genes has been observed when Akt1 is absent in mouse embryonic fibroblast (MEF) cells. In this study, we provide evidence that Akt1 regulates the 5' Hoxc gene expression by epigenetic modifications. Enrichment of histone H3K9 acetylation and a low level of the H3K27me3 mark were detected at the posterior 5' Hoxc loci when Akt1 is absent. A histone deacetylase (HDAC) inhibitor de-repressed 5' Hoxc gene expression when Akt1 is present, and a DNA demethylating reagent synergistically upregulated HDAC-induced 5' Hoxc gene expression. A knockdown study revealed that Hdac6 is mediated in the Hoxc12 repression through direct binding to the transcription start site (TSS) in the presence of Akt1. Co-immunoprecipitation analysis revealed that endogenous Akt1 directly interacted with Hdac6. Furthermore, exogenous Akt1 was enriched at the promoter region of the posterior Hoxc genes such as Hoxc11 and Hoxc12, not the Akt1-independent Hoxc5 and Hoxd10 loci. The regulation of the H3K27me3 mark by Ezh2 and Kdm6b at the 5' Hoxc gene promoter turned out to be Akt1 dependent. Taken together, these results suggest that Akt1 mediates the posterior 5' Hoxc gene expression through epigenetic modification such as histone methylation and acetylation, and partly through a direct binding to the promoter region of the 5' Hoxc genes and/or Hdac6 in mouse embryonic fibroblast cells.
Collapse
Affiliation(s)
- Kyoung-Ah Kong
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji Hoon Oh
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Youra Lee
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
31
|
Enhanced evolution by stochastically variable modification of epigenetic marks in the early embryo. Proc Natl Acad Sci U S A 2014; 111:6353-8. [PMID: 24733912 DOI: 10.1073/pnas.1402585111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Evolution by gene duplication is generally accepted as one of the crucial driving forces for the gain of new complexity and functions, but the formation of pseudogenes remains a problem for this mechanism. Here we expand on earlier ideas that epigenetic modifications can drive neo- and subfunctionalization in evolution by gene duplication. We explore the effects of stochastic epigenetic modifications on the evolution (and thus development) of complex organisms in a constant environment. Modeling is done both using a modified genetic drift analytical treatment and computer simulations, which were found to agree. A transposon silencing model is also explored. Some key assumptions made include (i) stochastic, incomplete removal (or addition) of repressive epigenetic marks takes place during a window(s) of opportunity in the zygote and early embryo; (ii) there is no statistical variation of the marks after the window closes; and (iii) the genes affected are sensitive to dosage. Our genetic drift treatment takes into account that after gene duplication the prevailing case upon which selection operates is a duplicate/singlet heterozygote; to the best of our knowledge, this has not been considered in previous treatments. We conclude from our modeling that stochastic epigenetic modifications, with rates consistent with experimental observation, can both increase the rate of gene fixation and decrease pseudogenization, thus dramatically improving the efficacy of evolution by gene duplication. We also find that a transposon silencing model is advantageous for fixation of recessive genes in diploid organisms, especially with large effective population sizes.
Collapse
|
32
|
Chemiluminescence resonance energy transfer biosensing platform for site-specific determination of DNA methylation and assay of DNA methyltransferase activity using exonuclease III-assisted target recycling amplification. Biosens Bioelectron 2014; 54:48-54. [DOI: 10.1016/j.bios.2013.10.050] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/30/2013] [Accepted: 10/22/2013] [Indexed: 01/06/2023]
|
33
|
Riviere G, Wu GC, Fellous A, Goux D, Sourdaine P, Favrel P. DNA methylation is crucial for the early development in the Oyster C. gigas. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:739-53. [PMID: 23877618 DOI: 10.1007/s10126-013-9523-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 06/04/2013] [Indexed: 05/02/2023]
Abstract
In vertebrates, epigenetic modifications influence gene transcription, and an appropriate DNA methylation is critical in development. Indeed, a precise temporal and spatial pattern of early gene expression is mandatory for a normal embryogenesis. However, such a regulation and its underlying mechanisms remain poorly understood in more distant organisms such as Lophotrochozoa. Thus, despite DNA in the oyster genome being methylated, the role of DNA methylation in development is unknown. To clarify this point, oyster genomic DNA was examined during early embryogenesis and found differentially methylated. Reverse transcriptase quantitative polymerase chain reaction indicated stage-specific levels of transcripts encoding DNA-methyltransferase (DNMT) and methyl-binding domain proteins. In addition, as highlighted by electronic microscopy and immunohistochemistry, the DNMT inhibitor 5-aza-cytidine induced alterations in the quantity and the localisation of methylated DNA and severe dose-dependent development alterations and was lethal after zygotic genome reinitiation. Furthermore, methyl-DNA-immunoprecipitation-quantitative polymerase chain reaction revealed that the transcription level of most of the homeobox gene orthologues examined, but not of the other early genes investigated, was inversely correlated with their specific DNA methylation. Altogether, our results demonstrate that DNA methylation influences gene expression in Crassostrea gigas and is critical for oyster development, possibly by specifically controlling the transcription level of homeobox orthologues. These findings provide evidence for the importance of epigenetic regulation of development in Lophotrochozoans and bring new insights into the early life of C. gigas, one of the most important aquaculture resources worldwide.
Collapse
Affiliation(s)
- Guillaume Riviere
- Biologie des Organismes Marins et des Ecosystèmes Associés (BioMEA) Esplanade de la paix, Université de Caen Basse-Normandie, 14032, Caen Cedex, France,
| | | | | | | | | | | |
Collapse
|
34
|
Cocozza S, Scala G, Miele G, Castaldo I, Monticelli A. A distinct group of CpG islands shows differential DNA methylation between replicas of the same cell line in vitro. BMC Genomics 2013; 14:692. [PMID: 24106769 PMCID: PMC4008136 DOI: 10.1186/1471-2164-14-692] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 10/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND CpG dinucleotide-rich genomic DNA regions, known as CpG islands (CGIs), can be methylated at their cytosine residues as an epigenetic mark that is stably inherited during cell mitosis. Differentially methylated regions (DMRs) are genomic regions showing different degrees of DNA methylation in multiple samples. In this study, we focused our attention on CGIs showing different DNA methylation between two culture replicas of the same cell line. RESULTS We used methylation data of 35 cell lines from the Encyclopedia of DNA Elements (ENCODE) consortium to identify CpG islands that were differentially methylated between replicas of the same cell line and denoted them Inter Replicas Differentially Methylated CpG islands (IRDM-CGIs). We identified a group of IRDM-CGIs that was consistently shared by different cell lines, and denoted it common IRDM-CGIs. X chromosome CGIs were overrepresented among common IRDM-CGIs. Autosomal IRDM-CGIs were preferentially located in gene bodies and intergenic regions had a lower G + C content, a smaller mean length, and a reduced CpG percentage. Functional analysis of the genes associated with autosomal IRDM-CGIs showed that many of them are involved in DNA binding and development. CONCLUSIONS Our results show that several specific functional and structural features characterize common IRDM-CGIs. They may represent a specific subset of CGIs that are more prone to being differentially methylated for their intrinsic characteristics.
Collapse
Affiliation(s)
- Sergio Cocozza
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", Naples, Italy.
| | | | | | | | | |
Collapse
|
35
|
Ambigapathy G, Zheng Z, Li W, Keifer J. Identification of a functionally distinct truncated BDNF mRNA splice variant and protein in Trachemys scripta elegans. PLoS One 2013; 8:e67141. [PMID: 23825634 PMCID: PMC3692439 DOI: 10.1371/journal.pone.0067141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/14/2013] [Indexed: 12/13/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) has a diverse functional role and complex pattern of gene expression. Alternative splicing of mRNA transcripts leads to further diversity of mRNAs and protein isoforms. Here, we describe the regulation of BDNF mRNA transcripts in an in vitro model of eyeblink classical conditioning and a unique transcript that forms a functionally distinct truncated BDNF protein isoform. Nine different mRNA transcripts from the BDNF gene of the pond turtle Trachemys scripta elegans (tBDNF) are selectively regulated during classical conditioning: exon I mRNA transcripts show no change, exon II transcripts are downregulated, while exon III transcripts are upregulated. One unique transcript that codes from exon II, tBDNF2a, contains a 40 base pair deletion in the protein coding exon that generates a truncated tBDNF protein. The truncated transcript and protein are expressed in the naïve untrained state and are fully repressed during conditioning when full-length mature tBDNF is expressed, thereby having an alternate pattern of expression in conditioning. Truncated BDNF is not restricted to turtles as a truncated mRNA splice variant has been described for the human BDNF gene. Further studies are required to determine the ubiquity of truncated BDNF alternative splice variants across species and the mechanisms of regulation and function of this newly recognized BDNF protein.
Collapse
Affiliation(s)
- Ganesh Ambigapathy
- Neuroscience Group, Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, South Dakota, United States of America
| | - Zhaoqing Zheng
- Neuroscience Group, Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, South Dakota, United States of America
| | - Wei Li
- Neuroscience Group, Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, South Dakota, United States of America
| | - Joyce Keifer
- Neuroscience Group, Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, South Dakota, United States of America
- * E-mail:
| |
Collapse
|
36
|
Østrup O, Andersen IS, Collas P. Chromatin-linked determinants of zygotic genome activation. Cell Mol Life Sci 2013; 70:1425-37. [PMID: 22965566 PMCID: PMC11113722 DOI: 10.1007/s00018-012-1143-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 12/20/2022]
Abstract
The merging of the maternal and paternal genomes into a single pronucleus after fertilization is accompanied by a remarkable reconfiguration of chromatin in the newly formed zygote. The first stages of embryonic chromatin remodeling take place in the absence of ongoing transcription, during a species-specific developmental time-frame. Once post-fertilization chromatin states are organized, zygotic genome activation (ZGA) is initiated, and embryonic transcripts gradually take control of development. We review here transitions in chromatin modifications associated with the onset of ZGA, and the role of transcription factors and DNA motifs in the regulation of ZGA. We propose a model of sequential chromatin remodeling events preceding ZGA, leading to the onset of embryonic transcription.
Collapse
Affiliation(s)
- Olga Østrup
- Stem Cell Epigenetics Laboratory, and Norwegian Center for Stem Cell Research, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Ingrid S. Andersen
- Stem Cell Epigenetics Laboratory, and Norwegian Center for Stem Cell Research, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Philippe Collas
- Stem Cell Epigenetics Laboratory, and Norwegian Center for Stem Cell Research, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317 Oslo, Norway
| |
Collapse
|
37
|
Abstract
Tissue-specific DNA methylation is found at promoters, enhancers, and CpG islands but also over larger genomic regions. In most human tissues, the vast majority of the genome is highly methylated (>70%). Recently, sequencing of bisulfite-treated DNA (MethylC-seq) has revealed large partially methylated domains (PMDs) in some human cell lines. PMDs cover up to 40% of the genome and are associated with gene repression and inactive chromatin marks. However, to date, only cultured cells and cancers have shown evidence for PMDs. Here, we performed MethylC-seq in full-term human placenta and demonstrate it is the first known normal tissue showing clear evidence of PMDs. We found that PMDs cover 37% of the placental genome, are stable throughout gestation and between individuals, and can be observed with lower sensitivity in Illumina 450K Infinium data. RNA-seq analysis confirmed that genes in PMDs are repressed in placenta. Using a hidden Markov model to map placental PMDs genome-wide and compare them to PMDs in other cell lines, we found that genes within placental PMDs have tissue-specific functions. For regulatory regions, methylation levels in promoter CpG islands are actually higher for genes within placental PMDs, despite the lower overall methylation of surrounding regions. Similar to PMDs, polycomb-regulated regions are hypomethylated but smaller and distinct from PMDs, with some being hypermethylated in placenta compared with other tissues. These results suggest that PMDs are a developmentally dynamic feature of the methylome that are relevant for understanding both normal development and cancer and may be of use as epigenetic biomarkers.
Collapse
|
38
|
Abstract
Methylation of the cytosine base in DNA, DNA methylation, is an essential epigenetic mark in mammals that contributes to the regulation of transcription. Several advances have been made in this area in recent years, leading to a leap forward in our understanding of how this pathway contributes to gene regulation during embryonic development, and the functional consequences of its perturbation in human disease. Critical to these advances is a comprehension of the genomic distribution of modified cytosine bases in unprecedented detail, drawing attention to genomic regions beyond gene promoters. In addition, we have a more complete understanding of the multifactorial manner by which DNA methylation influences gene regulation at the molecular level, and which genes rely directly on the DNA methylome for their normal transcriptional regulation. It is becoming apparent that a major role of DNA modification is to act as a relatively stable, and mitotically heritable, template that contributes to the establishment and maintenance of chromatin states. In this regard, interplay is emerging between DNA methylation and the PcG (Polycomb group) proteins, which act as evolutionarily conserved mediators of cell identity. In the present paper we review these aspects of DNA methylation, and discuss how a multifunctional view of DNA modification as an integral part of chromatin organization is influencing our understanding of this epigenetic mark's contribution to transcriptional regulation.
Collapse
|
39
|
Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, Ehrlich M. Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics 2013; 8:317-32. [PMID: 23417056 PMCID: PMC3669123 DOI: 10.4161/epi.23989] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 12/31/2022] Open
Abstract
Myogenic cell cultures derived from muscle biopsies are excellent models for human cell differentiation. We report the first comprehensive analysis of myogenesis-specific DNA hyper- and hypo-methylation throughout the genome for human muscle progenitor cells (both myoblasts and myotubes) and skeletal muscle tissue vs. 30 non-muscle samples using reduced representation bisulfite sequencing. We also focused on four genes with extensive hyper- or hypo-methylation in the muscle lineage (PAX3, TBX1, MYH7B/MIR499 and OBSCN) to compare DNA methylation, DNaseI hypersensitivity, histone modification, and CTCF binding profiles. We found that myogenic hypermethylation was strongly associated with homeobox or T-box genes and muscle hypomethylation with contractile fiber genes. Nonetheless, there was no simple relationship between differential gene expression and myogenic differential methylation, rather only for subsets of these genes, such as contractile fiber genes. Skeletal muscle retained ~30% of the hypomethylated sites but only ~3% of hypermethylated sites seen in myogenic progenitor cells. By enzymatic assays, skeletal muscle was 2-fold enriched globally in genomic 5-hydroxymethylcytosine (5-hmC) vs. myoblasts or myotubes and was the only sample type enriched in 5-hmC at tested myogenic hypermethylated sites in PAX3/CCDC140 andTBX1. TET1 and TET2 RNAs, which are involved in generation of 5-hmC and DNA demethylation, were strongly upregulated in myoblasts and myotubes. Our findings implicate de novo methylation predominantly before the myoblast stage and demethylation before and after the myotube stage in control of transcription and co-transcriptional RNA processing. They also suggest that, in muscle, TET1 or TET2 are involved in active demethylation and in formation of stable 5-hmC residues.
Collapse
MESH Headings
- 5-Methylcytosine/analogs & derivatives
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- CCCTC-Binding Factor
- Cardiac Myosins/genetics
- Cardiac Myosins/metabolism
- Case-Control Studies
- Cell Lineage/genetics
- Child
- Cytosine/analogs & derivatives
- Cytosine/metabolism
- DNA Methylation
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Developmental
- Genes, Homeobox
- Genome, Human
- Guanine Nucleotide Exchange Factors/genetics
- Guanine Nucleotide Exchange Factors/metabolism
- Histones/metabolism
- Humans
- Infant, Newborn
- Male
- Middle Aged
- Mixed Function Oxygenases
- Muscle Development/genetics
- Muscle Fibers, Skeletal/metabolism
- Muscle Proteins/genetics
- Muscle Proteins/metabolism
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Myoblasts/metabolism
- Myosin Heavy Chains/genetics
- Myosin Heavy Chains/metabolism
- PAX3 Transcription Factor
- Paired Box Transcription Factors/genetics
- Paired Box Transcription Factors/metabolism
- Protein Serine-Threonine Kinases
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Repressor Proteins/metabolism
- Rho Guanine Nucleotide Exchange Factors
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
- Transcription, Genetic
Collapse
Affiliation(s)
- Koji Tsumagari
- Program in Human Genetics and Tulane Cancer Center; Tulane Health Sciences Center; New Orleans, LA USA
| | - Carl Baribault
- Tulane Cancer Center and Department of Mathematics; Tulane Health Sciences Center and Tulane University; New Orleans, LA USA
| | | | | | - Jason Gertz
- HudsonAlpha Institute for Biotechnology; Huntsville, AL USA
| | | | - Melody Badoo
- Department of Pathology and Tulane Cancer Center; Tulane Health Sciences Center; New Orleans, LA USA
| | - Charlene M. Crain
- Center for Stem Cell Research and Regenerative Medicine; Tulane Health Sciences Center; New Orleans, LA USA
| | - Lingyun Song
- Institute for Genome Sciences & Policy; Duke University; Durham, NC USA
| | | | | | - Michelle Lacey
- Tulane Cancer Center and Department of Mathematics; Tulane Health Sciences Center and Tulane University; New Orleans, LA USA
| | - Melanie Ehrlich
- Program in Human Genetics; Tulane Cancer Center and Center for Bioinformatics and Genomics; Tulane Health Sciences Center; New Orleans, LA USA
| |
Collapse
|
40
|
Wang M, Xie H, Shrestha S, Sredni S, Morgan GA, Pachman LM. Methylation alterations of WT1 and homeobox genes in inflamed muscle biopsy samples from patients with untreated juvenile dermatomyositis suggest self-renewal capacity. ACTA ACUST UNITED AC 2013; 64:3478-85. [PMID: 22674142 DOI: 10.1002/art.34573] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
OBJECTIVE To determine the effect of methylation alteration in inflamed muscles from children with juvenile dermatomyositis (DM) and other idiopathic inflammatory myopathies (IIMs). METHODS Magnetic resonance imaging-directed diagnostic muscle biopsies yielded samples from 20 children with juvenile DM, which were used for genome-wide DNA methylation profiling, as were muscle biopsy samples from 4 healthy controls. Bisulfite treatment followed by pyrosequencing confirmed methylation status in juvenile DM and other IIMs. Immunohistochemistry defined localization and expression levels of WT1. RESULTS Comparison of genome-wide DNA methylation profiling between juvenile DM muscle and normal control muscle revealed 27 genes with a significant methylation difference between the groups. These genes were enriched with transcription factors and/or cell cycle regulators and were unrelated to duration of untreated disease. Six homeobox genes were among them; ALX4, HOXC11, HOXD3, and HOXD4 were hypomethylated, while EMX2 and HOXB1 were hypermethylated. WT1 was significantly hypomethylated in juvenile DM (Δβ = -0.41, P < 0.001). Bisulfite pyrosequencing verification in samples from 56 patients with juvenile DM confirmed the methylation alterations of these genes. Similar methylation alterations were observed in juvenile polymyositis (n = 5) and other IIMs (n = 9). Concordant with the other findings, WT1 protein was increased in juvenile DM muscle, with average positive staining of 11.6%, but was undetectable in normal muscle (P < 0.001). CONCLUSION These results suggest that affected muscles of children with juvenile DM and IIMs have the capacity to be repaired, and that homeobox and WT1 genes are epigenetically marked to facilitate this repair process, potentially suggesting new avenues of therapeutic intervention.
Collapse
Affiliation(s)
- Min Wang
- Children's Hospital of Chicago Research Center and Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | | | | | | | |
Collapse
|
41
|
|
42
|
Two Tunisian patients with Peters plus syndrome harbouring a novel splice site mutation in the B3GALTL gene that modulates the mRNA secondary structure. Gene 2012; 507:68-73. [DOI: 10.1016/j.gene.2012.06.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 05/26/2012] [Accepted: 06/21/2012] [Indexed: 11/18/2022]
|
43
|
Bell CG, Wilson GA, Butcher LM, Roos C, Walter L, Beck S. Human-specific CpG "beacons" identify loci associated with human-specific traits and disease. Epigenetics 2012; 7:1188-99. [PMID: 22968434 PMCID: PMC3469460 DOI: 10.4161/epi.22127] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Regulatory change has long been hypothesized to drive the delineation of the human phenotype from other closely related primates. Here we provide evidence that CpG dinucleotides play a special role in this process. CpGs enable epigenome variability via DNA methylation, and this epigenetic mark functions as a regulatory mechanism. Therefore, species-specific CpGs may influence species-specific regulation. We report non-polymorphic species-specific CpG dinucleotides (termed “CpG beacons”) as a distinct genomic feature associated with CpG island (CGI) evolution, human traits and disease. Using an inter-primate comparison, we identified 21 extreme CpG beacon clusters (≥ 20/kb peaks, empirical p < 1.0 × 10−3) in humans, which include associations with four monogenic developmental and neurological disease related genes (Benjamini-Hochberg corrected p = 6.03 × 10−3). We also demonstrate that beacon-mediated CpG density gain in CGIs correlates with reduced methylation in these species in orthologous CGIs over time, via human, chimpanzee and macaque MeDIP-seq. Therefore mapping into both the genomic and epigenomic space the identified CpG beacon clusters define points of intersection where a substantial two-way interaction between genetic sequence and epigenetic state has occurred. Taken together, our data support a model for CpG beacons to contribute to CGI evolution from genesis to tissue-specific to constitutively active CGIs.
Collapse
Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, UK.
| | | | | | | | | | | |
Collapse
|
44
|
Li W, Wu P, Zhang H, Cai C. Signal Amplification of Graphene Oxide Combining with Restriction Endonuclease for Site-Specific Determination of DNA Methylation and Assay of Methyltransferase Activity. Anal Chem 2012; 84:7583-90. [DOI: 10.1021/ac301990f] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Wen Li
- Jiangsu Key Laboratory of New Power Batteries, College
of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, College
of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Hui Zhang
- Jiangsu Key Laboratory of New Power Batteries, College
of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, College
of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| |
Collapse
|
45
|
Andersen IS, Reiner AH, Aanes H, Aleström P, Collas P. Developmental features of DNA methylation during activation of the embryonic zebrafish genome. Genome Biol 2012; 13:R65. [PMID: 22830626 PMCID: PMC3491385 DOI: 10.1186/gb-2012-13-7-r65] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 07/25/2012] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Zygotic genome activation (ZGA) occurs at the mid-blastula transition (MBT) in zebrafish and is a period of extensive chromatin remodeling. Genome-scale gametic demethylation and remethylation occurs after fertilization, during blastula stages, but how ZGA relates to promoter DNA methylation states is unknown. Using methylated DNA immunoprecipitation coupled to high-density microarray hybridization, we characterize genome-wide promoter DNA methylation dynamics before, during and after ZGA onset, in relation to changes in post-translational histone modifications and gene expression. RESULTS We show methylation of thousands of promoters before ZGA and additional methylation after ZGA, finding more dynamic methylation -1 to 0 kb upstream of the transcription start site than downstream. The MBT is marked by differential methylation of high and low CpG promoters, and we identify hypomethylated promoters that are mostly CG-rich and remain hypomethylated through the MBT. Hypomethylated regions constitute a platform for H3K4me3, whereas H3K9me3 preferentially associates with methylated regions. H3K27me3 associates with either methylation state depending on its coincidence with H3K4me3 or H3K9me3. Cohorts of genes differentially expressed through the MBT period display distinct promoter methylation patterns related to CG content rather than transcriptional fate. Lastly, although a significant proportion of genes methylated in sperm are unmethylated in embryos, over 90% of genes methylated in embryos are also methylated in sperm. CONCLUSIONS Our results suggest a pre-patterning of developmental gene expression potential by a combination of DNA hypomethylation and H3K4 trimethylation on CG-rich promoters, and are consistent with a transmission of DNA methylation states from gametes to early embryos.
Collapse
|
46
|
Schwartz TS, Perrin C, Wapstra E, Uller T, Olsson M. Complex selection associated with Hox genes in a natural population of lizards. J Evol Biol 2011; 24:2520-4. [PMID: 21883611 DOI: 10.1111/j.1420-9101.2011.02368.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hox genes are recognized for their explanatory power of bilateral development. However, relatively little is known about natural variation in, and the evolutionary dynamics of, Hox genes within wild populations. Utilizing a natural population of sand lizards (Lacerta agilis), we screened HoxA13 for genetic variation and an association with incidence of offspring malformations. We found significant effects of parental genetic similarity and offspring sex, and their interaction, on risk of hatching malformed as an offspring. We also found within population genetic variation in HoxA13, and identified a significant effect of a three-way interaction among Hox genotype, parental genetic similarity, and offspring sex on the risk of hatching malformation. Since malformed offspring in this population do not survive to maturity, this study reveals complex and ongoing selection associated with Hox genes in a wild reptile population. Importantly, this demonstrates the utility of natural populations in unveiling microevolutionary processes shaping variation in highly conserved genes.
Collapse
Affiliation(s)
- T S Schwartz
- School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia.
| | | | | | | | | |
Collapse
|
47
|
|
48
|
Talini G, Branciamore S, Gallori E. Ribozymes: Flexible molecular devices at work. Biochimie 2011; 93:1998-2005. [PMID: 21740954 DOI: 10.1016/j.biochi.2011.06.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 06/23/2011] [Indexed: 11/17/2022]
Abstract
The discovery of ribozymes, RNAs with catalytic activity, revealed the extraordinary characteristic of this molecule, and corroborated the idea that RNA was the first informative polymer. The "RNA world" hypothesis asserts that the DNA/RNA/PROTEIN world arose from an earlier RNA world in which were present only RNA molecules able to perform both of the two functions performed separately by DNA and proteins in the present-day cells: the ability to transfer genetic information and to carry out catalytic activity. The catalytic properties of ribozymes are exclusively due to the capacity of RNA molecules to assume particular structures. Moreover, the structural versatility of RNA can allow to a single RNA sequence to fold in more than one structure, able to perform more than one function. In the first part of this work we will discuss the RNA plasticity, focusing on "bifunctional" ribozymes isolated by in vitro selection experiments, and on the consequences of this plasticity in the prospective of the emergence of new specific functions. The possibility that one sequence could have more than one structure/function, greatly increase the evolutionary potential of RNA, and the capacity of RNA to switch from a structure/function to another is probably one of the reasons of the evolutionary success also in modern-day cells. Naturally occurring ribozymes discovered in contemporary cells, demonstrate the crucial role that ribozymes still have in the modern protein world. In the second part of this paper we will discuss the capacity of natural ribozymes to modulate gene expression making use of their exclusive catalytic properties. Moreover, we will consider the possibility of their ancient origin.
Collapse
Affiliation(s)
- Giulia Talini
- Laboratory of Cancer Genetics and Gene Transfer, Core Research Laboratory, Istituto Toscano Tumori, AOU Careggi, Viale Pieraccini 6, 50139 Florence, Italy
| | | | | |
Collapse
|