Genome-scale sequence data processing and epigenetic analysis of DNA methylation

Queen-worker caste dimorphism is a typical trait for honeybees (Apis mellifera). We previously showed a maternal effect on caste differentiation and queen development, where queens emerged from queen-cell eggs (QE) had higher quality than queens developed from worker cell eggs (WE). In this study, newly-emerged queens were reared from QE, WE, and 2-day worker larvae (2L). The thorax size and DNA methylation levels of queens were measured. We found that queens emerging from QE had significantly larger thorax length and width than WE and 2L. Epigenetic analysis showed that QE/2L comparison had the most different methylated genes (DMGs, 612) followed by WE/2L (473), and QE/WE (371). Interestingly, a great number of DMGs (42) were in genes belonging to mTOR, MAPK, Wnt, Notch, Hedgehog, FoxO, and Hippo signaling pathways that are involved in regulating caste differentiation, reproduction and longevity. This study proved that honeybee maternal effect causes epigenetic alteration regulating caste differentiation and queen development.

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DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola

Genes ◽

10.3390/genes10020137 ◽

2019 ◽

Vol 10 (2) ◽

pp. 137 ◽

Cited By ~ 16

Author(s):

Shenglin Liu ◽

Anne Aagaard ◽

Jesper Bechsgaard ◽

Trine Bilde

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Sequence Data ◽

Social Spider ◽

The Social ◽

Genome Bisulfite Sequencing ◽

Differential Gene ◽

Methylation Patterns ◽

Comparative Phylogenetic Analysis

Variation in DNA methylation patterns among genes, individuals, and populations appears to be highly variable among taxa, but our understanding of the functional significance of this variation is still incomplete. We here present the first whole genome bisulfite sequencing of a chelicerate species, the social spider Stegodyphus dumicola. We show that DNA methylation occurs mainly in CpG context and is concentrated in genes. This is a pattern also documented in other invertebrates. We present RNA sequence data to investigate the role of DNA methylation in gene regulation and show that, within individuals, methylated genes are more expressed than genes that are not methylated and that methylated genes are more stably expressed across individuals than unmethylated genes. Although no causal association is shown, this lends support for the implication of DNA CpG methylation in regulating gene expression in invertebrates. Differential DNA methylation between populations showed a small but significant correlation with differential gene expression. This is consistent with a possible role of DNA methylation in local adaptation. Based on indirect inference of the presence and pattern of DNA methylation in chelicerate species whose genomes have been sequenced, we performed a comparative phylogenetic analysis. We found strong evidence for exon DNA methylation in the horseshoe crab Limulus polyphemus and in all spider and scorpion species, while most Parasitiformes and Acariformes species seem to have lost DNA methylation.

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Comparing genome-scale DNA methylation and CNV marks between adult human cultured ITGA6+ testicular cells and seminomas to assess in vitro genomic stability

PLoS ONE ◽

10.1371/journal.pone.0230253 ◽

2020 ◽

Vol 15 (3) ◽

pp. e0230253 ◽

Cited By ~ 1

Author(s):

Robert B. Struijk ◽

Lambert C. J. Dorssers ◽

Peter Henneman ◽

Martin A. Rijlaarsdam ◽

Andrea Venema ◽

...

Keyword(s):

Dna Methylation ◽

Genomic Stability ◽

Adult Human ◽

Testicular Cells ◽

Genome Scale

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Reliable tumor detection by whole-genome methylation sequencing of cell-free DNA in cerebrospinal fluid of pediatric medulloblastoma

Science Advances ◽

10.1126/sciadv.abb5427 ◽

2020 ◽

Vol 6 (42) ◽

pp. eabb5427

Author(s):

Jia Li ◽

Sibo Zhao ◽

Minjung Lee ◽

Yue Yin ◽

Jin Li ◽

...

Keyword(s):

Dna Methylation ◽

Cerebrospinal Fluid ◽

Low Frequency ◽

Pediatric Medulloblastoma ◽

Oncogenic Mutations ◽

Genome Methylation ◽

Epigenetic Analysis ◽

Public Datasets ◽

Pediatric Brain ◽

Normal Cerebellum

Medulloblastoma (MB), the most common form of pediatric brain malignancy, has a low frequency of oncogenic mutations but pronouncedly abnormal DNA methylation changes. Epigenetic analysis of circulating cell-free tumor DNA (ctDNA) by liquid biopsy offers an approach for real-time monitoring of tumor status without tumor dissection. In this study, we identified 6598 differentially methylated CpGs in both MB tumors and the ctDNA isolated from matched cerebrospinal fluid (CSF) compared with normal cerebellum, which could be used to detect MB tumor occurrence and determine its subtype. Furthermore, DNA methylation changes in serial CSF samples could be used to monitor the treatment response and tumor recurrence. Integrating our data with large public datasets, we identified reliable MB DNA methylation signatures in ctDNA that have potential diagnostic and prognostic values. Our study sets the stage for exploiting epigenetic markers in CSF to improve the clinical management of patients with MB.

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