Epigenetic control of gene regulation in plants

Lauria, Massimiliano; Rossi, Vincenzo

doi:10.1016/j.bbagrm.2011.03.002

Cited by 114 publications

(98 citation statements)

References 117 publications

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“…This pattern has been proposed to play a role in transcriptional regulation, with moderately expressed genes being highly methylated in the gene body. An alternative role might lie in exon definition, since the majority of gene body methylation is found in exons (Saze and Kakutani, 2011), or the inhibition of transcriptional initiation from spurious promoters (Lauria and Rossi, 2011). Indeed, almost three-quarters of the differentially methylated sites identified in this experiment were found in an exon.…”

Section: Differential Methylation Targets 59 and 39 Edges Of Genic Rementioning

confidence: 99%

“…There are different ways in which gene body DNA methylation can influence RNA polymerase action and general transcript formation. First, DNA methylation could shield spurious transcript start sites within the gene in order to avoid the formation of truncated gene products, which could be deleterious to cellular function (Lauria and Rossi, 2011). Second, DNA methylation might simply identify which sequences within the transcript are exons and which are introns, as splicing generally coincides with transcription.…”

Section: Differential Methylation Targets 59 and 39 Edges Of Genic Rementioning

confidence: 99%

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Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

et al. 2014

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DNA methylation is an important and widespread epigenetic modification in plant genomes, mediated by DNA methyltransferases (DMTs). DNA methylation is known to play a role in genome protection, regulation of gene expression, and splicing and was previously associated with major developmental reprogramming in plants, such as vernalization and transition to flowering. Here, we show that DNA methylation also controls the growth processes of cell division and cell expansion within a growing organ. The maize (Zea mays) leaf offers a great tool to study growth processes, as the cells progressively move through the spatial gradient encompassing the division zone, transition zone, elongation zone, and mature zone. Opposite to de novo DMTs, the maintenance DMTs were transcriptionally regulated throughout the growth zone of the maize leaf, concomitant with differential CCGG methylation levels in the four zones. Surprisingly, the majority of differentially methylated sequences mapped on or close to gene bodies and not to repeat-rich loci. Moreover, especially the 59 and 39 regions of genes, which show overall low methylation levels, underwent differential methylation in a developmental context. Genes involved in processes such as chromatin remodeling, cell cycle progression, and growth regulation, were differentially methylated. The presence of differential methylation located upstream of the gene anticorrelated with transcript expression, while gene body differential methylation was unrelated to the expression level. These data indicate that DNA methylation is correlated with the decision to exit mitotic cell division and to enter cell expansion, which adds a new epigenetic level to the regulation of growth processes.DNA methylation is the covalent modification of nucleotides in DNA by the addition of a methyl group. In the nuclear genome of higher eukaryotes, 5-methylcytosine is the most important DNA modification (Goll and Bestor, 2005). It is a phenomenon of ancient origin predating plant-animal diversification. However, some differences exist between plant and animal methylome patterning and function, and DNA methylation has been found to be evolutionarily lost in a few species (Feng et al., 2010;Zemach et al., 2010). Eukaryotic DNA methylation is established by DNA methyltransferase (DMT) enzymes that transfer a methyl group from S-adenosyl Met to the fifth carbon of cytosine. These enzymes can largely be subdivided in maintenance and de novo DMTs, depending on whether the recognition site is already methylated or not. Maintenance DMTs conserve the methylation status of symmetrical (palindromic) sites after DNA replication, by recognizing the hemimethylated locus and methylating the newly synthesized strand. In plants, there are two types of maintenance DMTs: DNA METHYLTRANSFERASE (MET) and CHROMOMETHYLASE (CMT). The former methylates CG sites during DNA replication, whereas the latter methylates CHG (H = A, C, or T) sites located in chromatin in which histone 3 is dimethylated on Lys-9 (Goll and Bestor, 2005). De no...

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Section: Differential Methylation Targets 59 and 39 Edges Of Genic Rementioning

confidence: 99%

Section: Differential Methylation Targets 59 and 39 Edges Of Genic Rementioning

confidence: 99%

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

et al. 2014

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“…Third, the localization of some histone marks within the ZCN7 and ZCN8 loci was different than expected. That is, H3K4me3 was enriched in the 39 end, while it usually exhibits a peak in the 59 end region, and H3K27me3 accumulated in the 59 end region, while it usually is located in the gene body (Lauria and Rossi, 2011). Fig.…”

Section: Variation Of Zcn7 and Zcn8 Transcript Isoform Levels Under Fmentioning

confidence: 99%

“…Correlation of Histone Modifications in Line B73 ZCN7 and ZCN8 Chromatin with id1 Gene Activity Histone modifications are marks of chromatin transcriptional status (Lauria and Rossi, 2011). Therefore, we analyzed the histone profiles of the ZCN7 and ZCN8 genes in temperate maize to understand whether and how histone modifications are correlated with the id1-mediated activation of these genes.…”

Section: Variation Of Zcn7 and Zcn8 Transcript Isoform Levels Under Fmentioning

confidence: 99%

Florigen-Encoding Genes of Day-Neutral and Photoperiod-Sensitive Maize Are Regulated by Different Chromatin Modifications at the Floral Transition

Mascheretti

Turner²,

Brivio³

et al. 2015

Plant Physiol.

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ORCID IDs: 0000-0002-3136-9594 (J.C.); 0000-0001-9746-2583 (V.R.).The activity of the maize (Zea mays) florigen gene ZEA CENTRORADIALIS8 (ZCN8) is associated with the floral transition in both day-neutral temperate maize and short-day (SD)-requiring tropical maize. We analyzed transcription and chromatin modifications at the ZCN8 locus and its nearly identical paralog ZCN7 during the floral transition. This analysis was performed with day-neutral maize (Zea mays ssp. mays), where flowering is promoted almost exclusively via the autonomous pathway through the activity of the regulatory gene indeterminate1 (id1), and tropical teosinte (Zea mays ssp. parviglumis) under floral inductive and noninductive photoperiods. Comparison of ZCN7/ZCN8 histone modification profiles in immature leaves of nonflowering id1 mutants and teosinte grown under floral inhibitory photoperiods reveals that both id1 floral inductive activity and SD-mediated induction result in histone modification patterns that are compatible with the formation of transcriptionally competent chromatin environments. Specific histone modifications are maintained during leaf development and may represent a chromatin signature that favors the production of processed ZCN7/ZCN8 messenger RNA in florigen-producing mature leaf. However, whereas id1 function promotes histone H3 hyperacetylation, SD induction is associated with increased histone H3 dimethylation and trimethylation at lysine-4. In addition, id1 and SD differently affect the production of ZCN7/ZCN8 antisense transcript. These observations suggest that distinct mechanisms distinguish florigen regulation in response to autonomous and photoperiod pathways. Finally, the identical expression and histone modification profiles of ZCN7 and ZCN8 in response to floral induction suggest that ZCN7 may represent a second maize florigen.

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“…Analysis of histone modifications indicated that the release of NFC101/NFC102 binding correlated with an accumulation of H3ac and H3K4me2, which are characteristic marks for transcriptionally active chromatin states (Lauria and Rossi, 2011), and with a reduction of the H3K9me2 heterochromatin mark ( Figure 7B). …”

Section: Nfc101/nfc102 and Zcn8mentioning

confidence: 99%

The WD40-Repeat Proteins NFC101 and NFC102 Regulate Different Aspects of Maize Development through Chromatin Modification

Mascheretti¹,

Battaglia²,

Mainieri³

et al. 2013

The Plant Cell

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The maize (Zea mays) nucleosome remodeling factor complex component101 (nfc101) and nfc102 are putative paralogs encoding WD-repeat proteins with homology to plant and mammalian components of various chromatin modifying complexes. In this study, we generated transgenic lines with simultaneous nfc101 and nfc102 downregulation and analyzed phenotypic alterations, along with effects on RNA levels, the binding of NFC101/NFC102, and Rpd3-type histone deacetylases (HDACs), and histone modifications at selected targets. Direct NFC101/NFC102 binding and negative correlation with mRNA levels were observed for indeterminate1 (id1) and the florigen Zea mays CENTRORADIALIS8 (ZCN8), key activators of the floral transition. In addition, the abolition of NFC101/NFC102 association with repetitive sequences of different transposable elements (TEs) resulted in tissue-specific upregulation of nonpolyadenylated RNAs produced by these regions. All direct nfc101/nfc102 targets showed histone modification patterns linked to active chromatin in nfc101/nfc102 downregulation lines. However, different mechanisms may be involved because NFC101/NFC102 proteins mediate HDAC recruitment at id1 and TE repeats but not at ZCN8. These results, along with the pleiotropic effects observed in nfc101/nfc102 downregulation lines, suggest that NFC101 and NFC102 are components of distinct chromatin modifying complexes, which operate in different pathways and influence diverse aspects of maize development.

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Epigenetic control of gene regulation in plants

Cited by 114 publications

References 117 publications

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

Florigen-Encoding Genes of Day-Neutral and Photoperiod-Sensitive Maize Are Regulated by Different Chromatin Modifications at the Floral Transition

The WD40-Repeat Proteins NFC101 and NFC102 Regulate Different Aspects of Maize Development through Chromatin Modification

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