Position-dependent effects of cytosine methylation on<i>FWA</i>expression in<i>Arabidopsis thaliana</i>

Srikant, Thanvi; Wibowo, Anjar Tri; Schwab, Rebecca; Weigel, Detlef

doi:10.1101/774281

Cited by 4 publications

(6 citation statements)

References 36 publications

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“…In addition to studying how climate-mediated selection has shaped patterns of gene expression differentiation as a molecular phenotype, we also investigate how gene expression can serve as (56) or epi-allelic variation (80). Moreover, even though these models were informed by gene expression data collected in a single environment different from the conditions under which phenotype data were collected, incorporating this transcriptomic information still improved models of trait variation across multiple ecologically relevant conditions.…”

Section: Resultsmentioning

confidence: 99%

The scales and signatures of climate adaptation by theArabidopsistranscriptome

Colicchio¹,

Akman²,

Blackman³

2020

Preprint

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Clines in allele frequency and trait variation can be highly informative for understanding how populations have historically adapted to climate variation across landscapes. However, as a consequence of the many complexities inherent to this process, these climate-associated differentiation patterns can be confounded, misleading, or obscured. Molecular phenotypes like gene expression levels are a potentially valuable means for resolving these complexities. Their intermediate position between genomes and organismal traits and their interrelatedness structured by gene regulatory networks can help parse how different climatic factors contribute to unique components of range-wide or region-specific diversity patterns. Here, we demonstrate these explanatory values of gene expression variation through integrative analyses of transcriptomic data from 665 Arabidopsis thaliana accessions. Differentiation of co-expressed genes is often associated with source site climate. Although some patterns hold range-wide, many other gene expression clines are specific to particular ancestry groups, reflecting how broad-scale and local combinations of selective agents differentially resolve functional interrelationships between plant defense, drought tolerance, and life history traits. We also extend these analyses to parse how different factors explain climate-associated variation in flowering time and its plasticity. Expression of key regulators FLC and SOC1 strongly predicts time to flower, consistent with previous work, but our results also highlight novel relationships that indicate as yet unexplored climate-related connections between defense signaling and flowering. Finally, we show that integrative models combining genotype and gene expression information predict variation in flowering time under ecologically realistic conditions more accurately than models based on either source alone.

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Section: Resultsmentioning

confidence: 99%

The scales and signatures of climate adaptation by theArabidopsistranscriptome

Colicchio¹,

Akman²,

Blackman³

2020

Preprint

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“…DNA methylation with a similar repressive function is also found in the promoter of SBP-box and VITAMIN E 3 (VTE3) in tomatoes [19,20], OsAK1 [22] and DWARF1 [23] in rice, and CmWIP1 in melons [21]. The regulatory effect of promoter methylation in A. thaliana may also be sequence-or regionspecific; this has been shown in FWA, where methylation at tandem repeats overlapping the TSS can completely silence the gene but only has minimal effects on the transcription when found in upstream regions [116].…”

Section: Regulation Of Gene Expressions By Epialleles 41 Regulatory Function Of Epialleles In Proximity To Genesmentioning

confidence: 97%

“…This tool has been successfully used in different plant species to introduce methylation at the regulatory elements of various genes [115]. In A. thaliana, IR-hairpin constructs can efficiently induce methylation at the promoter of FWA [116], REPRESSOR OF SILENCING 1 (ROS1) [117], and distal enhancer region of FLOWERING LOCUS T (FT) [118], leading to the repression or complete silencing of the targeted genes.…”

Section: Epialleles Introduced By Epimutagenesismentioning

confidence: 99%

The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles

Srikant

Wibowo

2021

IJMS

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In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.

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“…FWA gets activated only in female gametophyte and endosperm by maternal imprinting. The FWA locus also is active in FWA mutant where hypomethylation occurs in the promoter of locus, resulting in delayed flowering ( Srikant et al, 2019 ).…”

Section: Biogenesis and Function Of Secondary Sirnasmentioning

confidence: 99%

Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology

et al. 2021

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The major components of RNA silencing include both transitive and systemic small RNAs, which are technically called secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to negatively regulate gene expression. The secondary siRNAs generated as a result of transitive silencing also play a substantial role in gene silencing especially in antiviral defense. In this review, we first describe the discovery and pathways of transitivity with emphasis on RNA-dependent RNA polymerases followed by description on the short range and systemic spread of silencing. We also provide an in-depth view on the various size classes of secondary siRNAs and their different roles in RNA silencing including their categorization based on their biogenesis. The other regulatory roles of secondary siRNAs in transgene silencing, virus-induced gene silencing, transitivity, and trans-species transfer have also been detailed. The possible implications and applications of systemic silencing and the different gene silencing tools developed are also described. The details on mobility and roles of secondary siRNAs derived from viral genome in plant defense against the respective viruses are presented. This entails the description of other compatible plant–virus interactions and the corresponding small RNAs that determine recovery from disease symptoms, exclusion of viruses from shoot meristems, and natural resistance. The last section presents an overview on the usefulness of RNA silencing for management of viral infections in crop plants.

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Position-dependent effects of cytosine methylation onFWAexpression inArabidopsis thaliana

Cited by 4 publications

References 36 publications

The scales and signatures of climate adaptation by theArabidopsistranscriptome

The scales and signatures of climate adaptation by theArabidopsistranscriptome

The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles

Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology

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