DREAM complex suppresses DNA methylation maintenance genes and precludes DNA hypermethylation

Ning, Yong-Qiang; Liu, Na; Lan, Ke-Ke; Su, Yin-Na; Li, Lin; Chen, She; He, Xin‐Jian

doi:10.1038/s41477-020-0710-7

Cited by 45 publications

(89 citation statements)

References 72 publications

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“…MET1 and VIM1/2/3 are required for the faithful transmission of mCG across cell cycles (Feng et al, 2010;Finnegan and Dennis, 1993;Ning et al, 2020;Woo et al, 2008) and accordingly had increased transcript levels in rapidly dividing early embryos that also correlated well with transcripts encoding cell-cycle activators throughout embryogenesis (Fig. 1A) (Hofmann et al, 2019;Papareddy et al, 2020).…”

Section: Cell Division Is Linked With Cg and Chg Methylation Through Distinct Mechanismsmentioning

confidence: 84%

“…DNA methylation is faithfully propagated across cell cycles by methyltransferases to ensure robust silencing of TEs (Borges et al, 2021;Law and Jacobsen, 2010;Mathieu et al, 2007;Ning et al, 2020;Probst et al, 2009;Saze et al, 2003). However, it is not well understood how DNA methyltransferases are regulated following periods of rapid division to prevent off-targeting of genes and their consequential repression.…”

Section: Discussionmentioning

confidence: 99%

“…The copyright holder for this preprint (which this version posted April 14, 2021. ; https://doi.org/10.1101/2021.04.14.439682 doi: bioRxiv preprint methylation and H3K9me2 also facilitate the stable propagation of silenced states through cell divisions (Jackson et al, 2002;Lindroth et al, 2001;Stroud et al, 2013Stroud et al, , 2014. METHYLTRANSFERASE 1 (MET1) maintains CG methylation through mitotic and meiotic cell divisions with high fidelity due to VARIANT IN METHYLATION 1/2/3 (VIM1/2/3) proteins that recognize hemi-methylated CG and recruit MET1 to methylate daughter strands (Feng et al, 2010;Finnegan and Dennis, 1993;Ning et al, 2020;Woo et al, 2008). CG methylation can also recruit RNA Polymerase IV complexes required to produce 24-nt small interfering RNAs (siRNAs) that are then loaded onto ARGONAUTE proteins and guide them to target loci by base-pairing with nucleic acids (Blevins et al, 2015;Herr et al, 2005;Papareddy et al, 2020;Zhai et al, 2015;Zilberman et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

“…Instead, CHH methylation of constitutive heterochromatin is mediated by CHRO-MOMETHYLASE 2 (CMT2) that binds to H3K9me2 deposited by KRYPTONITE (KYP) and closely related SUP-PRESSOR OF VARIATION 3-9 HOMOLOGUE PROTEIN 5/6 (SUVH5/6) methyltransferases (Stroud et al, 2014;Zemach et al, 2013). CHROMOMETHYLASE 3 (CMT3) also forms interlocking positive feedback loops with H3K9 methyltransferases (Du et al, 2012;Jackson et al, 2002;Lindroth et al, 2001), but is more closely associated with the cell cycle and mediates CHG methylation (Ning et al, 2020). CMT3-mediated CHG methylation is largely deposited on TEs.…”

Section: Introductionmentioning

confidence: 99%

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Repression of CHROMOMETHYLASE 3 Prevents Epigenetic Collateral Damage in Arabidopsis

Papareddy

Páldi

Smolka

et al. 2021

Preprint

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DNA methylation has evolved to silence mutagenic transposable elements (TEs) while typically avoiding the targeting of endogenous genes. Mechanisms that prevent DNA methyltransferases from ectopically methylating genes are expected to be of prime importance during periods of dynamic cell cycle activities including plant embryogenesis. However, virtually nothing is known regarding how DNA methyltransferase activities are precisely regulated during embryogenesis to prevent the induction of potentially deleterious and mitotically stable genic epimutations. Here, we report that microRNA-mediated repression of CHROMOMETHYLASE 3 (CMT3) and the chromatin features that CMT3 prefers help prevent ectopic methylation of thousands of genes during embryogenesis that can persist for weeks afterwards. Moreover, CMT3-induced ectopic methylation of genes undergoing transcriptional activation can reduce their corresponding transcript levels. Therefore, the repression of CMT3 prevents epigenetic collateral damage on endogenous genes. We also provide a model that may help reconcile conflicting viewpoints regarding the functions of gene-body methylation that occurs in nearly all flowering plants.

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Section: Cell Division Is Linked With Cg and Chg Methylation Through Distinct Mechanismsmentioning

confidence: 84%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Repression of CHROMOMETHYLASE 3 Prevents Epigenetic Collateral Damage in Arabidopsis

Papareddy

Páldi

Smolka

et al. 2021

Preprint

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“…DREAM target genes appear to extend beyond cell cycle genes. In a recent study, TCX5 was found to repress the expression of MET1 , CMT3 , DDM1 , KYP , and VIMs genes involved in maintenance of DNA methylation (Ning et al , ). TCX5 is redundant with its paralogue TCX6, and the double mutant tcx5, tcx6 exhibits increased levels of DNA methylation, primarily at CHG sites.…”

Section: Introductionmentioning

confidence: 99%

Roles of plant retinoblastoma protein: cell cycle and beyond

Desvoyes

Gutiérrez

2020

The EMBO Journal

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The human retinoblastoma (RB1) protein is a tumor suppressor that negatively regulates cell cycle progression through its interaction with members of the E2F/DP family of transcription factors. However, RB-related (RBR) proteins are an early acquisition during eukaryote evolution present in plant lineages, including unicellular algae, ancient plants (ferns, lycophytes, liverworts, mosses), gymnosperms, and angiosperms. The main RBR protein domains and interactions with E2Fs are conserved in all eukaryotes and not only regulate the G1/S transition but also the G2/M transition, as part of DREAM complexes. RBR proteins are also important for asymmetric cell division, stem cell maintenance, and the DNA damage response (DDR). RBR proteins play crucial roles at every developmental phase transition, in association with chromatin factors, as well as during the reproductive phase during female and male gametes production and embryo development. Here, we review the processes where plant RBR proteins play a role and discuss possible avenues of research to obtain a full picture of the multifunctional roles of RBR for plant life.

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DREAM a little dREAM of DRM: Model organisms and conservation of DREAM‐like complexes

Hoareau,

Rincheval‐Arnold,

Gaumer

et al. 2023

BioEssays

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DREAM complexes are transcriptional regulators that control the expression of hundreds to thousands of target genes involved in the cell cycle, quiescence, differentiation, and apoptosis. These complexes contain many subunits that can vary according to the considered target genes. Depending on their composition and the nature of the partners they recruit, DREAM complexes control gene expression through diverse mechanisms, including chromatin remodeling, transcription cofactor and factor recruitment at various genomic binding sites. This complexity is particularly high in mammals. Since the discovery of the first dREAM complex (drosophila Rb, E2F, and Myb) in Drosophila melanogaster, model organisms such as Caenorhabditis elegans, and plants allowed a deeper understanding of the processes regulated by DREAM‐like complexes. Here, we review the conservation of these complexes. We discuss the contribution of model organisms to the study of DREAM‐mediated transcriptional regulatory mechanisms and their relevance in characterizing novel activities of DREAM complexes.

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DREAM complex suppresses DNA methylation maintenance genes and precludes DNA hypermethylation

Cited by 45 publications

References 72 publications

Repression of CHROMOMETHYLASE 3 Prevents Epigenetic Collateral Damage in Arabidopsis

Repression of CHROMOMETHYLASE 3 Prevents Epigenetic Collateral Damage in Arabidopsis

Roles of plant retinoblastoma protein: cell cycle and beyond

DREAM a little dREAM of DRM: Model organisms and conservation of DREAM‐like complexes

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