Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis

2014 ◽  
Vol 81 (2) ◽  
pp. 268-281 ◽  
Author(s):  
Hongxing Yang ◽  
Fang Chang ◽  
Chenjiang You ◽  
Jie Cui ◽  
Genfeng Zhu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Structure ◽  
Flower Development ◽  
Whole Genome ◽  
Gene Structure And Expression ◽  
Methylation Patterns

scholarly journals Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird

2020 ◽  
Vol 60 (6) ◽  
pp. 1517-1530 ◽  
Author(s):  
Kees van Oers ◽  
Bernice Sepers ◽  
William Sies ◽  
Fleur Gawehns ◽  
Koen J F Verhoeven ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Exploratory Behavior ◽  
Parus Major ◽  
Phenotypic Selection ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Behavioral Differences ◽  
Heritable Variation ◽  
Genome Wide ◽  
Methylation Patterns

Synopsis The search for the hereditary mechanisms underlying quantitative traits traditionally focused on the identification of underlying genomic polymorphisms such as single-nucleotide polymorphisms. It has now become clear that epigenetic mechanisms, such as DNA methylation, can consistently alter gene expression over multiple generations. It is unclear, however, if and how DNA methylation can stably be transferred from one generation to the next and can thereby be a component of the heritable variation of a trait. In this study, we explore whether DNA methylation responds to phenotypic selection using whole-genome and genome-wide bisulfite approaches. We assessed differential erythrocyte DNA methylation patterns between extreme personality types in the Great Tit (Parus major). For this, we used individuals from a four-generation artificial bi-directional selection experiment and siblings from eight F2 inter-cross families. We find no differentially methylated sites when comparing the selected personality lines, providing no evidence for the so-called epialleles associated with exploratory behavior. Using a pair-wise sibling design in the F2 intercrosses, we show that the genome-wide DNA methylation profiles of individuals are mainly explained by family structure, indicating that the majority of variation in DNA methylation in CpG sites between individuals can be explained by genetic differences. Although we found some candidates explaining behavioral differences between F2 siblings, we could not confirm this with a whole-genome approach, thereby confirming the absence of epialleles in these F2 intercrosses. We conclude that while epigenetic variation may underlie phenotypic variation in behavioral traits, we were not able to find evidence that DNA methylation can explain heritable variation in personality traits in Great Tits.

scholarly journals Comparison of Whole-Genome DNA Methylation Patterns in Whole Blood, Saliva, and Lymphoblastoid Cell Lines

2012 ◽  
Vol 43 (2) ◽  
pp. 168-176 ◽  
Author(s):  
Tara M. Thompson ◽  
Duaa Sharfi ◽  
Maria Lee ◽  
Carolyn M. Yrigollen ◽  
Oksana Yu Naumova ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Cell Lines ◽  
Whole Blood ◽  
Lymphoblastoid Cell Lines ◽  
Whole Genome ◽  
Methylation Patterns

scholarly journals Human muscle carbonic anhydrase: gene structure and DNA methylation patterns in fetal and adult tissues.

1987 ◽  
Vol 1 (6) ◽  
pp. 594-602 ◽  
Author(s):  
J Lloyd ◽  
C Brownson ◽  
S Tweedie ◽  
J Charlton ◽  
Y H Edwards
Keyword(s):  
Dna Methylation ◽  
Carbonic Anhydrase ◽  
Gene Structure ◽  
Human Muscle ◽  
Adult Tissues ◽  
Methylation Patterns ◽  
Carbonic Anhydrase Gene

Whole-genome DNA methylation patterns and complex associations with gene expression associated with anthocyanin biosynthesis in apple fruit skin

Planta ◽  
2019 ◽  
Vol 250 (6) ◽  
pp. 1833-1847 ◽  
Author(s):  
Wen-Fang Li ◽  
Gai-Xing Ning ◽  
Juan Mao ◽  
Zhi-Gang Guo ◽  
Qi Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Anthocyanin Biosynthesis ◽  
Apple Fruit ◽  
Whole Genome ◽  
Fruit Skin ◽  
Methylation Patterns

scholarly journals Epigenetic Response of Yarrowia lipolytica to Stress: Tracking Methylation Level and Search for Methylation Patterns via Whole-Genome Sequencing

2021 ◽  
Vol 9 (9) ◽  
pp. 1798
Author(s):  
Monika Kubiak-Szymendera ◽  
Leszek P. Pryszcz ◽  
Wojciech Białas ◽  
Ewelina Celińska
Keyword(s):  
Dna Methylation ◽  
Whole Genome Sequencing ◽  
Yarrowia Lipolytica ◽  
Genome Sequencing ◽  
Methylation Level ◽  
Epigenetic Modification ◽  
Bacterial Species ◽  
Whole Genome ◽  
Immuno Assay ◽  
Methylation Patterns

DNA methylation is a common, but not universal, epigenetic modification that plays an important role in multiple cellular processes. While definitely settled for numerous plant, mammalian, and bacterial species, the genome methylation in different fungal species, including widely studied and industrially-relevant yeast species, Yarrowia lipolytica, is still a matter of debate. In this paper, we report a differential DNA methylation level in the genome of Y. lipolytica subjected to sequential subculturing and to heat stress conditions. To this end, we adopted repeated batch bioreactor cultivations of Y. lipolytica subjected to thermal stress in specific time intervals. To analyze the variation in DNA methylation between stressed and control cultures, we (a) quantified the global DNA methylation status using an immuno-assay, and (b) studied DNA methylation patterns through whole-genome sequencing. Primarily, we demonstrated that 5 mC modification can be detected using a commercial immuno-assay, and that the modifications are present in Y. lipolytica’s genome at ~0.5% 5 mC frequency. On the other hand, we did not observe any changes in the epigenetic response of Y. lipolytica to heat shock (HS) treatment. Interestingly, we identified a general phenomenon of decreased 5 mC level in Y. lipolytica’s genome in the stationary phase of growth, when compared to a late-exponential epigenome. While this study provides an insight into the subculturing stress response and adaptation to the stress at epigenetic level by Y. lipolytica, it also leaves an open question of inability to detect any genomic DNA methylation level (either in CpG context or context-less) through whole-genome sequencing. The results of ONT sequencing, suggesting that 5 mC modification is either rare or non-existent in Y. lipolytica genome, are contradicted with the results of the immunoassay.

scholarly journals Comparative Analyses of Sperm DNA Methylomes Among Three Commercial Pig Breeds Reveal Vital Hypomethylated Regions Associated With Spermatogenesis and Embryonic Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Siqian Chen ◽  
Shuli Liu ◽  
Siyuan Mi ◽  
Wenlong Li ◽  
Shengli Zhang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Complex Traits ◽  
Bisulfite Sequencing ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Large White ◽  
Pig Breeds ◽  
Sperm Dna ◽  
Public Data ◽  
Methylation Patterns

Identifying epigenetic changes is essential for an in-depth understanding of phenotypic diversity and pigs as the human medical model for anatomizing complex diseases. Abnormal sperm DNA methylation can lead to male infertility, fetal development failure, and affect the phenotypic traits of offspring. However, the whole genome epigenome map in pig sperm is lacking to date. In this study, we profiled methylation levels of cytosine in three commercial pig breeds, Landrace, Duroc, and Large White using whole-genome bisulfite sequencing (WGBS). The results showed that the correlation of methylation levels between Landrace and Large White pigs was higher. We found that 1,040–1,666 breed-specific hypomethylated regions (HMRs) were associated with embryonic developmental and economically complex traits for each breed. By integrating reduced representation bisulfite sequencing (RRBS) public data of pig testis, 1743 conservated HMRs between sperm and testis were defined, which may play a role in spermatogenesis. In addition, we found that the DNA methylation patterns of human and pig sperm showed high similarity by integrating public data from WGBS and chromatin immunoprecipitation sequencing (ChIP-seq) in other mammals, such as human and mouse. We identified 2,733 conserved HMRs between human and pig involved in organ development and brain-related traits, such as NLGN1 (neuroligin 1) containing a conserved-HMR between human and pig. Our results revealed the similarities and diversity of sperm methylation patterns among three commercial pig breeds and between human and pig. These findings are beneficial for elucidating the mechanism of male fertility, and the changes in commercial traits that undergo strong selection.

scholarly journals Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Yang Zhou ◽  
Shuli Liu ◽  
Yan Hu ◽  
Lingzhao Fang ◽  
Yahui Gao ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Whole Genome ◽  
Tissue Specific ◽  
Dna Methylation Profiling ◽  
Methylation Patterns ◽  
Methylation Profiling

scholarly journals DNA methylation signatures of duplicate gene evolution in angiosperms

2020 ◽  
Author(s):  
Sunil K. Kenchanmane Raju ◽  
S. Marshall Ledford ◽  
Chad E. Niederhuth
Keyword(s):  
Dna Methylation ◽  
Gene Evolution ◽  
Gene Dosage ◽  
Single Gene ◽  
Constitutive Expression ◽  
Duplicate Gene ◽  
Duplicate Genes ◽  
Whole Genome ◽  
Gene Duplicates ◽  
Methylation Patterns

ABSTRACTGene duplications have greatly shaped the gene content of plants. Multiple factors, such as the epigenome, can shape the subsequent evolution of duplicate genes and are the subject of ongoing study. We analyze genic DNA methylation patterns in 43 angiosperm species and 928 Arabidopsis thaliana ecotypes to finding differences in the association of whole-genome and single-gene duplicates with genic DNA methylation patterns. Whole-genome duplicates were enriched for patterns associated with higher gene expression and depleted for patterns of non-CG DNA methylation associated with gene silencing. Single-gene duplicates showed variation in DNA methylation patterns based on modes of duplication (tandem, proximal, transposed, and dispersed) and species. Age of gene duplication was a key factor in the DNA methylation of single-gene duplicates. In single-gene duplicates, non-CG DNA methylation patterns associated with silencing were younger, less conserved, and enriched for presence-absence variation. In comparison, DNA methylation patterns associated with constitutive expression were older and more highly conserved. Surprisingly, across the phylogeny, genes marked by non-CG DNA methylation were enriched for duplicate pairs with evidence of positive selection. We propose that DNA methylation has a role in maintaining gene-dosage balance and silencing by non-CG methylation and may facilitate the evolutionary fate of duplicate genes.

Examination of the dynamics of global DNA methylation pattern establishment during spermatogenesiss

2007 ◽  
Vol 30 (4) ◽  
pp. 90
Author(s):  
Kirsten Niles ◽  
Sophie La Salle ◽  
Christopher Oakes ◽  
Jacquetta Trasler
Keyword(s):  
Dna Methylation ◽  
Germ Cell ◽  
Germ Cells ◽  
Epigenetic Modification ◽  
Methylation Pattern ◽  
Chromosome 9 ◽  
Specific Gene ◽  
Global Methylation ◽  
Dna Methylation Pattern ◽  
Methylation Patterns

Background: DNA methylation is an epigenetic modification involved in gene expression, genome stability, and genomic imprinting. In the male, methylation patterns are initially erased in primordial germ cells (PGCs) as they enter the gonadal ridge; methylation patterns are then acquired on CpG dinucleotides during gametogenesis. Correct pattern establishment is essential for normal spermatogenesis. To date, the characterization and timing of methylation pattern acquisition in PGCs has been described using a limited number of specific gene loci. This study aimed to describe DNA methylation pattern establishment dynamics during male gametogenesis through global methylation profiling techniques in a mouse model. Methods: Using a chromosome based approach, primers were designed for 24 regions spanning chromosome 9; intergenic, non-repeat, non-CpG island sequences were chosen for study based on previous evidence that these types of sequences are targets for testis-specific methylation events. The percent methylation was determined in each region by quantitative analysis of DNA methylation using real-time PCR (qAMP). The germ cell-specific pattern was determined by comparing methylation between spermatozoa and liver. To examine methylation in developing germ cells, spermatogonia from 2 day- and 6 day-old Oct4-GFP (green fluorescent protein) mice were isolated using fluorescence activated cell sorting. Results: As compared to liver, four loci were hypomethylated and five loci were hypermethylated in spermatozoa, supporting previous results indicating a unique methylation pattern in male germ cells. Only one region was hypomethylated and no regions were hypermethylated in day 6 spermatogonia as compared to mature spermatozoa, signifying that the bulk of DNA methylation is established prior to type A spermatogonia. The methylation in day 2 spermatogonia, germ cells that are just commencing mitosis, revealed differences of 15-20% compared to day 6 spermatogonia at five regions indicating that the most crucial phase of DNA methylation acquisition occurs prenatally. Conclusion: Together, these studies provide further evidence that germ cell methylation patterns differ from those in somatic tissues and suggest that much of methylation at intergenic sites is acquired during prenatal germ cell development. (Supported by CIHR)

Sign in / Sign up

Export Citation Format

Share Document