+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia

Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia

Plos Biology 14(7): E1002500

Gene expression divergence between closely related species could be attributed to both cis- and trans- DNA sequence changes during evolution, but it is unclear how the evolutionary dynamics of epigenetic marks are regulated. In eutherian mammals, biparental DNA methylation marks are erased and reset during gametogenesis, resulting in paternal or maternal imprints, which lead to genomic imprinting. Whether DNA methylation reprogramming exists in insects is not known. Wasps of the genus Nasonia are non-social parasitoids that are emerging as a model for studies of epigenetic processes in insects. In this study, we quantified allele-specific expression and methylation genome-wide in Nasonia vitripennis and Nasonia giraulti and their reciprocal F1 hybrids. No parent-of-origin effect in allelic expression was found for >8,000 covered genes, suggesting a lack of genomic imprinting in adult Nasonia. As we expected, both significant cis- and trans- effects are responsible for the expression divergence between N. vitripennis and N. giraulti. Surprisingly, all 178 differentially methylated genes are also differentially methylated between the two alleles in F1 hybrid offspring, recapitulating the parental methylation status with nearly 100% fidelity, indicating the presence of strong cis-elements driving the target of gene body methylation. In addition, we discovered that total and allele-specific expression are positively correlated with allele-specific methylation in a subset of the differentially methylated genes. The 100% cis-regulation in F1 hybrids suggests the methylation machinery is conserved and DNA methylation is targeted by cis features in Nasonia. The lack of genomic imprinting and parent-of-origin differentially methylated regions in Nasonia, together with the stable inheritance of methylation status between generations, suggests either a cis-regulatory motif for methylation at the DNA level or highly stable inheritance of an epigenetic signal in Nasonia.

Please choose payment method:

(PDF emailed within 1 workday: $29.90)

Accession: 057160140

Download citation: RISBibTeXText

PMID: 27380029

Related references

Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta. American Journal of Human Genetics 99(5): 1045-1058, 2017

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Blood 123(17): E79-E89, 2014

Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern. Bmc Genomics 18(1): 336, 2017

Allele specific expression analysis of the porcine blood transcriptome reveals extensive cis-regulation in immunity-related genes. Journal of Animal Science 94: 168-169, 2016

Neuron-specific methylome analysis reveals epigenetic regulation and tau-related dysfunction of BRCA1 in Alzheimer's disease. Proceedings of the National Academy of Sciences of the United States of America 114(45): E9645-E9654, 2017

Array-based DNA methylation profiling in male infertility reveals allele-specific DNA methylation in PIWIL1 and PIWIL2. Fertility and Sterility 101(4): 1097-1103.E1, 2014

Integrative analysis of methylome and transcriptome reveals the importance of unmethylated CpGs in non-CpG island gene activation. Biomed Research International 2013: 785731, 2014

Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia. Epigenetics 10(9): 882-890, 2016

Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple. Scientific Reports 7: 17167, 2017

Quantitative allele-specific expression and DNA methylation analysis of H19, IGF2 and IGF2R in the human placenta across gestation reveals H19 imprinting plasticity. Plos One 7(12): E51210, 2013

DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands. Epigenomics 8(10): 1367-1387, 2016

Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma. Cancer Medicine 4(7): 1079-1090, 2016

H19-DMR allele-specific methylation analysis reveals epigenetic heterogeneity of CTCF binding site 6 but not of site 5 in head-and-neck carcinomas: a pilot case-control analysis. International Journal of Molecular Medicine 17(2): 397-404, 2006

Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression. Proceedings of the National Academy of Sciences of the United States of America 112(50): E7022-9, 2016

Allele-specific methylation analysis on upstream promoter region of H19 by methylation-specific PCR with confronting two-pair primers. International Journal of Oncology 25(5): 1273-1278, 2004