Gene body DNA methylation in plants

Bewick, Adam J.; Schmitz, Robert J.

doi:10.1016/j.pbi.2016.12.007

Cited by 311 publications

(354 citation statements)

References 48 publications

(108 reference statements)

Supporting

Mentioning

320

Contrasting

Unclassified

Order By: Relevance

“…Possibly, GBM changes slowly, only in response to sustained changes in transcription. This hypothesis is consistent with observations of mutant lines for met1 methyltransferase in Arabidopsis, where genome-wide loss of GBM returns only slowly following reintroduction of the wild-type gene (27)(28). If this were the case, GBM would integrate over acute transcriptional fluctuations and might better represent the developing acclimatization response compared to the one-time 'snapshot' provided by transcriptomic assays.…”

Section: Missing Mechanismsupporting

confidence: 85%

Role of gene body methylation in coral acclimatization and adaptation

Dixon

Liao

Bay

et al. 2017

Preprint

View full text Add to dashboard Cite

Despite widespread taxonomic representation, the function of gene body methylation (GBM) remains uncertain. One hypothesis is that GBM mediates phenotypic plasticity. To investigate this hypothesis, we performed whole-genome methylation and transcriptome profiling on reciprocally transplanted colony fragments of the reef-building coral Acropora millepora. GBM was only slightly affected by transplantation but these small changes correlated with coral fitness in the new environment. Specifically, for transplanted corals, similarity in GBM patterns to native corals positively correlated with growth rate, as well as carbohydrate, protein, lipid and endosymbiont content. Between populations, elevated GBM positively correlated with transcription, supporting previous findings that GBM is associated with stable and active transcription. Contrary to expectations however, changes in transcription as a result of transplantation did not correlate with changes in GBM and did not predict fitness. This indicates that on physiological time scales GBM is not directly coupled to transcription, leaving open the question about the mechanism linking GBM to fitness during acclimatization.

show abstract

Section: Missing Mechanismsupporting

confidence: 85%

Role of gene body methylation in coral acclimatization and adaptation

Dixon

Liao

Bay

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…). High levels of gene body methylation is also found in highly expressed genes in plants; while currently the function is unknown, Zilberman () hypothesizes that it functions to stabilize expression by reducing histone variants and Bewick and Schmitz () hypothesize that it is a by‐product of transposable element silencing.…”

Section: Discussionmentioning

confidence: 99%

Methylation and gene expression differences between reproductive and sterile bumblebee workers

2019

View full text Add to dashboard Cite

Phenotypic plasticity is the production of multiple phenotypes from a single genome and is notably observed in social insects. Multiple epigenetic mechanisms have been associated with social insect plasticity, with DNA methylation being explored to the greatest extent. DNA methylation is thought to play a role in caste determination in Apis mellifera, and other social insects, but there is limited knowledge on its role in other bee species. In this study, we analyzed whole genome bisulfite sequencing and RNA‐seq data sets from head tissue of reproductive and sterile castes of the eusocial bumblebee Bombus terrestris. We found that genome‐wide methylation in B. terrestris is similar to other holometabolous insects and does not differ between reproductive castes. We did, however, find differentially methylated genes between castes, which are enriched for multiple biological processes including reproduction. However, we found no relationship between differential methylation and differential gene expression or differential exon usage between castes. Our results also indicate high intercolony variation in methylation. These findings suggest that methylation is associated with caste differences but may serve an alternate function, other than direct caste determination in this species. This study provides the first insights into the nature of a bumblebee caste‐specific methylome as well as its interaction with gene expression and caste‐specific alternative splicing, providing greater understanding of the role of methylation in phenotypic plasticity within social bee species. Future experimental work is needed to determine the function of methylation and other epigenetic mechanisms in insects.

show abstract

“…RdDM and the methytransferase, CMT2, define the two complementary pathways for the establishment and maintenance of m CHH in Arabidopsis (Zemach et al ). Interestingly, however, CMT2 seems to be absent from the maize genome, leaving RdDM as the main pathway to mediate m CHH (Zemach et al ; Bewick and Schmitz ). DDM1 in Arabidopsis is involved in CMT2 ‐dependent m CHH, but not in the RdDM pathway (Zemach et al ).…”

Section: Discussionmentioning

confidence: 99%

Decrease in DNA methylation 1 (DDM1) is required for the formation of ^mCHH islands in maize

Long

Xia

Liu

et al. 2019

JIPB

View full text Add to dashboard Cite

DNA methylation plays a crucial role in suppressing mobilization of transposable elements and regulation of gene expression. A number of studies have indicated that DNA methylation pathways and patterns exhibit distinct properties in different species, including Arabidopsis, rice, and maize. Here, we characterized the function of DDM1 in regulating genome‐wide DNA methylation in maize. Two homologs of ZmDDM1 are abundantly expressed in the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development. We establish that ZmDDM1 is critical for DNA methylation, at CHG sites, and to a lesser extent at CG sites, in heterochromatic regions, and unexpectedly, it is required for the formation of mCHH islands. In addition, ZmDDM1 is indispensable for the presence of 24‐nt siRNA, suggesting its involvement in the RdDM pathway. Our results provide novel insight into the role of ZmDDM1 in regulating the formation of mCHH islands, via the RdDM pathway maize, suggesting that, in comparison to Arabidopsis, maize may have adopted distinct mechanisms for regulating mCHH.

show abstract

Gene body DNA methylation in plants

Cited by 311 publications

References 48 publications

Role of gene body methylation in coral acclimatization and adaptation

Role of gene body methylation in coral acclimatization and adaptation

Methylation and gene expression differences between reproductive and sterile bumblebee workers

Decrease in DNA methylation 1 (DDM1) is required for the formation of ^mCHH islands in maize

Contact Info

Product

Resources

About

Gene body DNA methylation in plants

Cited by 311 publications

References 48 publications

Role of gene body methylation in coral acclimatization and adaptation

Role of gene body methylation in coral acclimatization and adaptation

Methylation and gene expression differences between reproductive and sterile bumblebee workers

Decrease in DNA methylation 1 (DDM1) is required for the formation of mCHH islands in maize

Contact Info

Product

Resources

About

Decrease in DNA methylation 1 (DDM1) is required for the formation of ^mCHH islands in maize