scholarly journals A variably imprinted epiallele impacts seed development

2018 ◽  
Author(s):  
Daniela Pignatta ◽  
Katherine Novitzky ◽  
P.R. V. Satyaki ◽  
Mary Gehring
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Genetic Variation ◽  
Seed Development ◽  
Phenotypic Variation ◽  
Strong Association ◽  
Endosperm Development ◽  
Flowering Plants ◽  
Epigenetic Variation ◽  
Epigenetic Information

AbstractThe contribution of epigenetic variation to phenotypic variation is unclear. Imprinted genes, because of their strong association with epigenetic modifications, represent an opportunity for the discovery of such phenomena. In mammals and flowering plants, a subset of genes are expressed from only one parental allele in a process called gene imprinting. Imprinting is associated with differential DNA methylation and chromatin modifications between parental alleles. In flowering plants imprinting occurs in a seed tissue – endosperm. Proper endosperm development is essential for the production of viable seeds. We previously showed that in Arabidopsis thaliana intraspecific imprinting variation is correlated with naturally occurring DNA methylation polymorphisms. Here, we investigated the mechanisms and function of allele-specific imprinting of the class IV homeodomain-Leucine zipper (HD-ZIP) transcription factor HDG3. In imprinted strains, HDG3 is expressed primarily from the methylated paternally inherited allele. We manipulated the methylation state of endogenous HDG3 in a non-imprinted strain and demonstrated that methylation of a proximal transposable element is sufficient to promote HDG3 expression and imprinting. Gain of HDG3 imprinting was associated with earlier endosperm cellularization and changes in seed weight. These results indicate that epigenetic variation alone is sufficient to explain imprinting variation and demonstrate that epialleles can underlie variation in seed development phenotypes.Author SummaryThe contribution of genetic variation to phenotypic variation is well-established. By contrast, it is unknown how frequently epigenetic variation causes differences in organismal phenotypes. Epigenetic information is closely associated with but not encoded in the DNA sequence. In practice, it is challenging to disentangle genetic variation from epigenetic variation, as what appears to be epigenetic variation might have an underlying genetic basis. DNA methylation is one form of epigenetic information. HDG3 encodes an endosperm specific transcription factor that exists in two states in A. thaliana natural populations: methylated and expressed and hypomethylated and repressed. We show that pure epigenetic variation is sufficient to explain expression variation of HDG3 – a naturally lowly expressed allele can be switched to a higher expressed state by adding DNA methylation. We also show that expression of HDG3 in strains where it is normally hypomethylated and relatively repressed causes a seed development phenotype. These data indicate that naturally circulating epialleles have consequences for seed phenotypic variation.

scholarly journals Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 291
Author(s):  
Biao Ni ◽  
Jian You ◽  
Jiangnan Li ◽  
Yingda Du ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Soil Properties ◽  
Changbai Mountains ◽  
Epigenetic Variation ◽  
Geographical Distance ◽  
Mantel Tests ◽  
Epigenetic Diversity ◽  
Different Populations

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

scholarly journals Seed Genome Hypomethylated Regions Are Enriched In Transcription Factor Genes

2018 ◽  
Author(s):  
Min Chen ◽  
Jer-Young Lin ◽  
Jungim Hur ◽  
Julie M. Pelletier ◽  
Russell Baden ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Seed Development ◽  
Mammalian Cells ◽  
Fatty Acid Biosynthesis ◽  
Developmental Stages ◽  
Storage Proteins ◽  
Seed Formation ◽  
Epigenetic Events ◽  
Transcription Factor Genes

AbstractThe precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators, such as ABI3 and FUS3, are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes, and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from post-fertilization through dormancy and germination for regions that contain < 5% or < 0.4% bulk methylation in CG-, CHG-, and CHH-contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5 to 76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor genes, and other developmental genes, that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue - and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development - probably by the action of specific transcription factors and epigenetic events at the chromatin level.SignificanceWe scanned soybean and Arabidopsis seed genomes for hypomethylated regions, or DNA Methylation Valleys (DMVs), present in mammalian cells. A significant fraction of seed genomes contain DMV regions that have < 5% bulk DNA methylation, or, in many cases, no detectable DNA methylation. Methylation levels of seed DMVs do not vary detectably during seed development with respect to time, region, and tissue, and are present prior to fertilization. Seed DMVs are enriched in transcription factor genes and other genes critical for seed development, and are also decorated with histone marks that fluctuate with developmental stage, resembling in significant ways their animal counterparts. We conclude that many genes playing important roles in seed formation are regulated in the absence of detectable DNA methylation events, and suggest that selective action of transcriptional activators and repressors, as well as chromatin epigenetic events play important roles in making a seed - particularly embryo formation.

scholarly journals Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles

PLoS Genetics ◽  
2020 ◽  
Vol 16 (11) ◽  
pp. e1009189
Author(s):  
Alejandro Martin-Trujillo ◽  
Nihir Patel ◽  
Felix Richter ◽  
Bharati Jadhav ◽  
Paras Garg ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Genetic Variation ◽  
Dna Binding ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Ctcf Binding ◽  
Factor Binding ◽  
Rare Genetic Variation

Although DNA methylation is the best characterized epigenetic mark, the mechanism by which it is targeted to specific regions in the genome remains unclear. Recent studies have revealed that local DNA methylation profiles might be dictated by cis-regulatory DNA sequences that mainly operate via DNA-binding factors. Consistent with this finding, we have recently shown that disruption of CTCF-binding sites by rare single nucleotide variants (SNVs) can underlie cis-linked DNA methylation changes in patients with congenital anomalies. These data raise the hypothesis that rare genetic variation at transcription factor binding sites (TFBSs) might contribute to local DNA methylation patterning. In this work, by combining blood genome-wide DNA methylation profiles, whole genome sequencing-derived SNVs from 247 unrelated individuals along with 133 predicted TFBS motifs derived from ENCODE ChIP-Seq data, we observed an association between the disruption of binding sites for multiple TFs by rare SNVs and extreme DNA methylation values at both local and, to a lesser extent, distant CpGs. While the majority of these changes affected only single CpGs, 24% were associated with multiple outlier CpGs within ±1kb of the disrupted TFBS. Interestingly, disruption of functionally constrained sites within TF motifs lead to larger DNA methylation changes at nearby CpG sites. Altogether, these findings suggest that rare SNVs at TFBS negatively influence TF-DNA binding, which can lead to an altered local DNA methylation profile. Furthermore, subsequent integration of DNA methylation and RNA-Seq profiles from cardiac tissues enabled us to observe an association between rare SNV-directed DNA methylation and outlier expression of nearby genes. In conclusion, our findings not only provide insights into the effect of rare genetic variation at TFBS on shaping local DNA methylation and its consequences on genome regulation, but also provide a rationale to incorporate DNA methylation data to interpret the functional role of rare variants.

scholarly journals Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels

2014 ◽  
Author(s):  
Nicholas E. Banovich ◽  
Xun Lan ◽  
Graham McVicker ◽  
Bryce van de Geijn ◽  
Jacob F. Degner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Genetic Variation ◽  
Histone Modifications ◽  
Transcription Factor Binding ◽  
Dnase I ◽  
Expression Levels ◽  
Factor Binding ◽  
Quantitative Changes

AbstractDNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ∼300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at an FDR of 10%) 13,915 cis methylation QTLs (meQTLs)—i.e., CpG sites in which changes in DNA methylation are associated with genetic variation at proximal loci. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNase I accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest that genetic variants may lead to coordinated molecular changes in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that SNPs that change predicted TF binding affinities are significantly enriched for associations with DNA methylation at nearby CpGs.Author SummaryDNA methylation is an important epigenetic mark that contributes to many biological processes including the regulation of gene expression. Genetic variation has been associated with quantitative changes in DNA methylation (meQTLs). We identified thousands of meQTLs using an assay that allowed us to measure methylation levels at around 300 thousand cytosines. We found that meQTLs are enriched with loci that is also associated with quantitative changes in gene expression, DNase I hypersensitivity, PolII occupancy, and a number of histone marks. This suggests that many molecular events are likely regulated in concert. Finally, we found that changes in transcription factor binding as well as transcription factor abundance are associated with changes in DNA methylation near transcription factor binding sites. This work contributes to our understanding of the regulation of DNA methylation in the larger context of gene regulatory landscape.

scholarly journals Genomic asymmetry of the Brassica napus seed: Epigenetic contributions of DNA methylation and small RNAs to subgenome bias

2020 ◽  
Author(s):  
Dylan J. Ziegler ◽  
Deirdre Khan ◽  
Nadège Pulgar-Vidal ◽  
Isobel A.P. Parkin ◽  
Stephen J. Robinson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brassica Napus ◽  
Seed Development ◽  
Epigenetic Regulation ◽  
Small Rnas ◽  
Flowering Plants ◽  
Genetic History ◽  
History Of ◽  
Syntenic Regions

AbstractPolyploidy has predominated the genetic history of the angiosperms, and allopolyploidy is known to have contributed to the vast speciation of flowering plants. Brassica napus, one of the world’s most important oilseeds, is one such polyploid species originating from the interspecific hybridization of Brassica rapa (An) and Brassica oleracea (Cn). Nascent amphidiploids must balance progenitor genomes during reproduction, though the role of epigenetic regulation in subgenome maintenance is unknown. The seed is the pivotal developmental transition into the new sporophytic generation and as such undergoes substantial epigenetic modifications. We investigated subgenome bias between the An and Cn subgenomes as well as across syntenic regions by profiling DNA methylation and siRNAs characteristic of B. napus seed development. DNA methylation and siRNA accumulation were prevalent in the Cn subgenome and most pronounced early during seed morphogenesis. Hypermethylation during seed maturation was most pronounced on non-coding elements, including promoters, repetitive elements, and siRNAs. Methylation on siRNA clusters was more prevalent in syntenic regions of the Cn subgenome and implies selective silencing of genomic loci of the seed. Together, we find compelling evidence for the asymmetrical epigenetic regulation of the An and Cn subgenomes of Brassica napus across seed development.

scholarly journals Inheritance of DNA methylation differences in the mangrove Rhizophora mangle

2020 ◽  
Author(s):  
Jeannie Mounger ◽  
M. Teresa Boquete ◽  
Marc W. Schmid ◽  
Renan Granado ◽  
Marta H. Robertson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
Gulf Coast ◽  
Natural Populations ◽  
Rhizophora Mangle ◽  
Genotyping By Sequencing ◽  
Foundation Species ◽  
Ecosystem Functions ◽  
Epigenetic Variation ◽  
Epigenetic Diversity

AbstractThe capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and non-genetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the non-genetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions, and is potentially threatened by climate change. Several studies have documented landscape level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of non-genetic variation. To assess one type of non-genetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing or epiGBS) to address the following questions: a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? b) How are genetic and epigenetic variation structured within and among populations? c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field and that a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.

scholarly journals Epigenetic Variation May Compensate for Decreased Genetic Variation with Introductions: A Case Study Using House Sparrows (Passer domesticus) on Two Continents

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Aaron W. Schrey ◽  
Courtney A. C. Coon ◽  
Michael T. Grispo ◽  
Mohammed Awad ◽  
Titus Imboma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Phenotypic Variation ◽  
Passer Domesticus ◽  
Phenotypic Traits ◽  
Epigenetic Variation ◽  
House Sparrows ◽  
Introduction History ◽  
Outlier Loci

Epigenetic mechanisms impact several phenotypic traits and may be important for ecology and evolution. The introduced house sparrow (Passer domesticus) exhibits extensive phenotypic variation among and within populations. We screened methylation in populations from Kenya and Florida to determine if methylation varied among populations, varied with introduction history (Kenyan invasion <50 years old, Florida invasion ~150 years old), and could potentially compensate for decrease genetic variation with introductions. While recent literature has speculated on the importance of epigenetic effects for biological invasions, this is the first such study among wild vertebrates. Methylation was more frequent in Nairobi, and outlier loci suggest that populations may be differentiated. Methylation diversity was similar between populations, in spite of known lower genetic diversity in Nairobi, which suggests that epigenetic variation may compensate for decreased genetic diversity as a source of phenotypic variation during introduction. Our results suggest that methylation differences may be common among house sparrows, but research is needed to discern whether methylation impacts phenotypic variation.

scholarly journals The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways

2019 ◽  
Author(s):  
Yunduan Li ◽  
Songlin Zhang ◽  
Ruzhuang Dong ◽  
Li Wang ◽  
Jin Yao ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Signaling Pathways ◽  
Seed Development ◽  
Cytosine Methylation ◽  
Fruit Size ◽  
Homeobox Gene ◽  
Seed Number ◽  
Homeodomain Transcription Factors

Abstract Background: The homeobox transcription factor has a diversity of functions during plant growth and development process. Previous transcriptome analyses of seed development in grape hybrids suggested that specific homeodomain transcription factors are involved in seed development in seedless cultivars. However, the molecular mechanism of homeobox gene regulating seed development in grape is rarely reported. Results: Here, we report that the grapevine VvHB58 gene, encoding a homeodomain-leucine zipper (HD-Zip I) transcription factor, participates in regulating fruit size and seed number. The VvHB58 gene was differentially expressed during seed development between seedless and seeded cultivars. Subcellular localization assays revealed that the VvHB58 protein was located in the nucleus. Transgenic expression of VvHB58 in tomato led to loss of apical dominance, a reduction in fruit pericarp expansion, reduced fruit size and seed number, and larger endosperm cells. Analysis of the cytosine methylation levels within the VvHB58 promoter indicated that the differential expression during seed development between seedless and seeded grapes may be caused by different transcriptional regulatory mechanisms rather than promoter DNA methylation. Measurements of five classic endogenous hormones and expression analysis of hormone-related genes between VvHB58 transgenic and nontransgenic control plants showed that expression of VvHB58 resulted in significant changes in auxin, gibberellin and ethylene signaling pathways. Additionally, several DNA methylation-related genes were expressed differentially during seed development stages in seedless and seeded grapes, suggesting changes in methylation levels during seed development may be associated with seed abortion. Conclusion: VvHB58 has a potential function in regulating fruit and seed development by impacting multiple hormonal pathways. These results expand understanding of homeodomain transcription factors and potential regulatory mechanism of seed development in grapevine, and provided insights into molecular breeding for grapes.

scholarly journals The seagrass methylome memorizes heat stress and is associated with variation in stress performance among clonal shoots

2019 ◽  
Author(s):  
A Jueterbock ◽  
C Boström ◽  
James A Coyer ◽  
JL Olsen ◽  
M Kopp ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
Heat Stress ◽  
Conservation Management ◽  
Clonal Plants ◽  
Photosynthetic Performance ◽  
Epigenetic Variation ◽  
Stress Resilience ◽  
Seagrass Meadows ◽  
Methylation Patterns

AbstractEvolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management considers genetic variation as the ultimate measure of a population’s ability to survive over time. However, clonal plants are among the oldest living organisms on our planet. Here, we test the hypothesis that clonal seagrass meadows display epigenetic variation that complements genetic variation as a source of phenotypic variation. In a clonal meadow of the seagrass Zostera marina we characterized DNA methylation among 42 shoots. We also sequenced the whole genome of 10 shoots to correlate methylation patterns with photosynthetic performance under exposure to, and recovery from 27°C, while controlling for somatic mutations. Here, we show for the first time that clonal seagrass shoots display DNA methylation variation that is associated with variation in fitness-related traits: photosynthetic performance and heat stress resilience. The co-variation in DNA methylation and phenotype may be linked via gene expression because methylation patterns varied in functionally relevant genes involved in photosynthesis, and in the repair and prevention of heat-induced protein damage. A >five week epigenetic heat stress memory may heat-harden previously heat-exposed shoots. While genotypic diversity has been shown to enhance stress resilience in seagrass meadows, we suggest that epigenetic variation plays a similar role in meadows dominated by a single genotype. Consequently, conservation management of clonal plants should consider epigenetic variation as indicator of resilience and stability, and restoration efforts may benefit from stress-priming transplanted seeds or shoots.

scholarly journals Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jing Xu ◽  
Guo Chen ◽  
Peter J. Hermanson ◽  
Qiang Xu ◽  
Changshuo Sun ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
Association Analysis ◽  
Phenotypic Variation ◽  
Biological Significance ◽  
Population Level ◽  
Unique Information ◽  
Genome Wide ◽  
Methylation Profiling ◽  
Methylation Variation

Abstract Background DNA methylation can provide a source of heritable information that is sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling and the roles of DNA methylation in shaping diversity of both gene expression and phenotypes are hotly debated. Here, we investigate the genetic basis and biological functions of DNA methylation at a population scale in maize. Results We perform targeted DNA methylation profiling for a diverse panel of 263 maize inbred genotypes. All genotypes show similar levels of DNA methylation globally, highlighting the importance of DNA methylation in maize development. Nevertheless, we identify more than 16,000 differentially methylated regions (DMRs) that are distributed across the 10 maize chromosomes. Genome-wide association analysis with high-density genetic markers reveals that over 60% of the DMRs are not tagged by SNPs, suggesting the presence of unique information in DMRs. Strong associations between DMRs and the expression of many genes are identified in both the leaf and kernel tissues, pointing to the biological significance of methylation variation. Association analysis with 986 metabolic traits suggests that DNA methylation is associated with phenotypic variation of 156 traits. There are some traits that only show significant associations with DMRs and not with SNPs. Conclusions These results suggest that DNA methylation can provide unique information to explain phenotypic variation in maize.

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