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Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish. G3-GENES GENOMES GENETICS 2016; 6:3581-3591. [PMID: 27646705 PMCID: PMC5100857 DOI: 10.1534/g3.116.032243] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter methylation of duplicate genes generally decreased with evolutionary time as measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated, while the other was unmethylated across nine different datasets we studied. Moreover, one motif enriched in promoter methylated duplicate genes tended to be bound by the transcription repression factor FOXD3, whereas a motif enriched in the promoter unmethylated sequences interacted with the transcription activator Sp1, indicating a complex interaction between the genomic environment and epigenome. Besides, body-methylated genes showed longer length than body-unmethylated genes. Overall, our results suggest that DNA methylation is highly important in the differential expression and evolution of duplicate genes in zebrafish.
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Davis AP, Benninghoff AD, Thomas AJ, Sessions BR, White KL. DNA methylation of the LIN28 pseudogene family. BMC Genomics 2015; 16:287. [PMID: 25884154 PMCID: PMC4404226 DOI: 10.1186/s12864-015-1487-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 03/25/2015] [Indexed: 12/01/2022] Open
Abstract
Background DNA methylation directs the epigenetic silencing of selected regions of DNA, including the regulation of pseudogenes, and is widespread throughout the genome. Pseudogenes are decayed copies of duplicated genes that have spread throughout the genome by transposition. Pseudogenes are transcriptionally silenced by DNA methylation, but little is known about how pseudogenes are targeted for methylation or how methylation levels are maintained in different tissues. Results We employed bisulfite next generation sequencing to examine the methylation status of the LIN28 gene and four processed pseudogenes derived from LIN28. The objective was to determine whether LIN28 pseudogenes maintain the same pattern of methylation as the parental gene or acquire a methylation pattern independent of the gene of origin. In this study, we determined that the methylation status of LIN28 pseudogenes does not resemble the pattern evident for the LIN28 gene, but rather these pseudogenes appear to acquire methylation patterns independent of the parental gene. Furthermore, we observed that methylation levels of the examined pseudogenes correlate to the location of insertion within the genome. LIN28 pseudogenes inserted into gene bodies were highly methylated in all tissues examined. In contrast, pseudogenes inserted into genomic regions that are not proximal to genes were differentially methylated in various tissue types. Conclusions Our analysis suggests that Lin28 pseudogenes do not aquire patterns of tissue-specific methylation as for the parental gene, but rather are methylated in patterns specific to the local genomic environment into which they were inserted. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1487-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aaron P Davis
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA.
| | - Abby D Benninghoff
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA. .,School of Veterinary Medicine, Utah State University, Logan, UT, USA. .,USTAR Applied Nutrition Research, Utah State University, Logan, UT, USA.
| | - Aaron J Thomas
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA.
| | - Benjamin R Sessions
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA.
| | - Kenneth L White
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322-4815, USA. .,School of Veterinary Medicine, Utah State University, Logan, UT, USA.
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Hesson LB, Ward RL. Discrimination of pseudogene and parental gene DNA methylation using allelic bisulfite sequencing. Methods Mol Biol 2014; 1167:265-274. [PMID: 24823784 DOI: 10.1007/978-1-4939-0835-6_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Determining the methylation status of genes with pseudogenes can be technically challenging due to sequence homology. High sequence homology can result in the amplification of both pseudogene and parental gene alleles, potentially leading to data misinterpretation. Allelic bisulfite sequencing allows for detection of the methylation status of individual alleles at nucleotide resolution and represents the most reliable method for discriminating pseudogene and parental gene sequences. Here, we discuss important points that should be considered when investigating pseudogene and parental gene methylation status and we describe the method of allelic bisulfite sequencing, including assay design.
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Affiliation(s)
- Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Kensington, Sydney, NSW, 2227, Australia,
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Parrish RR, Day JJ, Lubin FD. Direct bisulfite sequencing for examination of DNA methylation with gene and nucleotide resolution from brain tissues. ACTA ACUST UNITED AC 2013; Chapter 7:Unit 7.24. [PMID: 22752896 DOI: 10.1002/0471142301.ns0724s60] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA methylation is an epigenetic modification that is essential for the development and mature function of the central nervous system. Due to the relevance of this modification to the transcriptional control of gene expression, it is often necessary to examine changes in DNA methylation patterns with both gene and single-nucleotide resolution. Here, we describe an in-depth basic protocol for direct bisulfite sequencing of DNA isolated from brain tissue, which will permit direct assessment of methylation status at individual genes as well as individual cytosine molecules/nucleotides within a genomic region. This method yields analysis of DNA methylation patterns that is robust, accurate, and reproducible, thereby allowing insights into the role of alterations in DNA methylation in brain tissue.
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Affiliation(s)
- R Ryley Parrish
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
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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: 74] [Impact Index Per Article: 6.7] [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.
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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
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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
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Meagher RB, Müssar KJ. The influence of DNA sequence on epigenome-induced pathologies. Epigenetics Chromatin 2012; 5:11. [PMID: 22818522 PMCID: PMC3439399 DOI: 10.1186/1756-8935-5-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 07/20/2012] [Indexed: 01/13/2023] Open
Abstract
Clear cause-and-effect relationships are commonly established between genotype and the inherited risk of acquiring human and plant diseases and aberrant phenotypes. By contrast, few such cause-and-effect relationships are established linking a chromatin structure (that is, the epitype) with the transgenerational risk of acquiring a disease or abnormal phenotype. It is not entirely clear how epitypes are inherited from parent to offspring as populations evolve, even though epigenetics is proposed to be fundamental to evolution and the likelihood of acquiring many diseases. This article explores the hypothesis that, for transgenerationally inherited chromatin structures, "genotype predisposes epitype", and that epitype functions as a modifier of gene expression within the classical central dogma of molecular biology. Evidence for the causal contribution of genotype to inherited epitypes and epigenetic risk comes primarily from two different kinds of studies discussed herein. The first and direct method of research proceeds by the examination of the transgenerational inheritance of epitype and the penetrance of phenotype among genetically related individuals. The second approach identifies epitypes that are duplicated (as DNA sequences are duplicated) and evolutionarily conserved among repeated patterns in the DNA sequence. The body of this article summarizes particularly robust examples of these studies from humans, mice, Arabidopsis, and other organisms. The bulk of the data from both areas of research support the hypothesis that genotypes predispose the likelihood of displaying various epitypes, but for only a few classes of epitype. This analysis suggests that renewed efforts are needed in identifying polymorphic DNA sequences that determine variable nucleosome positioning and DNA methylation as the primary cause of inherited epigenome-induced pathologies. By contrast, there is very little evidence that DNA sequence directly determines the inherited positioning of numerous and diverse post-translational modifications of histone side chains within nucleosomes. We discuss the medical and scientific implications of these observations on future research and on the development of solutions to epigenetically induced disorders.
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Affiliation(s)
- Richard B Meagher
- Genetics Department, Davison Life Sciences Building, University of Georgia, Athens, GA, 30605, USA.
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Chang AYF, Liao BY. DNA methylation rebalances gene dosage after mammalian gene duplications. Mol Biol Evol 2011; 29:133-44. [PMID: 21821837 DOI: 10.1093/molbev/msr174] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although gene duplication plays a major role in organismal evolution, it may also lead to gene dosage imbalance, thereby having an immediate adverse effect on an organism's fitness. Investigating the evolution of the expression patterns of genes that duplicated after the divergence of rodents and primates, we confirm that adaptive evolution has been involved in dosage rebalance after gene duplication. To understand mechanisms underlying this process, we examined 1) microRNA (miRNA)-mediated gene regulation, 2) cis-regulatory sequence modifications, and 3) DNA methylation. Neither miRNA-mediated regulation nor cis-regulatory changes was found to be associated with expression reduction of duplicate genes. By contrast, duplicate genes, especially lowly expressed copies, were heavily methylated in the upstream region. However, for duplicate genes encoding proteins that are members of macromolecular complexes, heavy methylation in the genic region was not consistently observed. This result held after controlling potential confounding factors, such as enrichment in functional categories. Our results suggest that during mammalian evolution, DNA methylation plays a dominant role in dosage rebalance after gene duplication by inhibiting transcription initiation of duplicate genes.
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Affiliation(s)
- Andrew Ying-Fei Chang
- Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
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Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray. Genomics 2011; 97:214-22. [PMID: 21211562 DOI: 10.1016/j.ygeno.2010.12.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 10/20/2010] [Accepted: 12/18/2010] [Indexed: 12/12/2022]
Abstract
The Illumina Infinium HumanMethylation27 BeadChip (Illumina 27k) microarray is a high-throughput platform capable of interrogating the human DNA methylome. In a search for autosomal sex-specific DNA methylation using this microarray, we discovered autosomal CpG loci showing significant methylation differences between the sexes. However, we found that the majority of these probes cross-reacted with sequences from sex chromosomes. Moreover, we determined that 6-10% of the microarray probes are non-specific and map to highly homologous genomic sequences. Using probes targeting different CpGs that are exact duplicates of each other, we investigated the precision of these repeat measurements and concluded that the overall precision of this microarray is excellent. In addition, we identified a small number of probes targeting CpGs that include single-nucleotide polymorphisms. Overall, our findings address several technical issues associated with the Illumina 27k microarray that, once considered, will enhance the analysis and interpretation of data generated from this platform.
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