Identification of putative Arabidopsis DEMETER target genes by GeneChip analysis

Ohr, Hyonhwa; Bui, Anhthu Q.; Le, Brandon H.; Fischer, Robert L.; Choi, Yeonhee

doi:10.1016/j.bbrc.2007.10.092

Cited by 10 publications

(3 citation statements)

References 33 publications

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“…DNA demethylation by DME occurs during reproductive development and is required for genomic imprinting and seed viability. DML enzymes demethylate approximately 179 loci, of which nearly 80% are genes [55][56][57][58].…”

Section: Resultsmentioning

confidence: 99%

<i>Hordeum vulgare</i> miežių lapų stabilių DNR baltymų kompleksų baltymų sudėties analizė

Bielskienė¹,

Bagdoniene

Labeikytė³

et al. 2009

Biologija

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Tightly bound to DNA proteins (TBP) are a protein group that remains attached to DNA with covalent or non-covalent bonds after its deproteinisation [1,2]. TBP have been found in DNA of numerous evolutionary distant species [3][4][5]. Some of these TBP proteins have been characterized in Ehrlich ascites [6-8] and yeast (Saccharomyces cerevisiae) [9] cells. The aim of this work was to characterize TBP proteins in the first leaves of barley (Hordeum vulgare) shoots by the MALDI TOF-TOF mass-spectrometry (MS) analysis. We have identified that most of these proteins (WRKY transcription factors 16 and 52, MADS-box transcription factor 26, Squamosa promoter-binding-like protein 16, Scarecrow-like protein 9, TGA4, TEOSINTE BRANCHED 1) are transcription factors playing important roles in the development and coping with either biotic or abiotic stress in plants. Various barley TBP (above transcription factors, DEMETER-like protein 2, HAC12, RAD51, Ty3-gypsy retrotransposon, protein kinases, serpins) participate in chromatin rearrangement and the regulation of gene expression.

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Section: Resultsmentioning

confidence: 99%

<i>Hordeum vulgare</i> miežių lapų stabilių DNR baltymų kompleksų baltymų sudėties analizė

Bielskienė¹,

Bagdoniene

Labeikytė³

et al. 2009

Biologija

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“…RNA interference directed against H1‐3 affected the imprinting mechanism and DNA methylation (Rea et al ., ). A search for DME downstream targets by analysis of DME overexpression revealed strong upregulation of H1‐3 (Ohr et al ., ). Therefore, downregulation of H1‐3 might also contribute to detection of ET‐mediated DNA methylation differences.…”

Section: Discussionmentioning

confidence: 99%

EFFECTOR OF TRANSCRIPTION factors are novel plant‐specific regulators associated with genomic DNA methylation in Arabidopsis

et al. 2018

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Summary Plant‐specific EFFECTORS OF TRANSCRIPTION ( ET ) are characterised by a variable number of highly conserved ET repeats, which are involved in zinc and DNA binding. In addition, ET s share a GIY ‐ YIG domain, involved in DNA nicking activity. It was hypothesised that ET s might act as epigenetic regulators. Here, methylome, transcriptome and phenotypic analyses were performed to investigate the role of ET factors and their involvement in DNA methylation in Arabidopsis thaliana . Comparative DNA methylation and transcriptome analyses in flowers and seedlings of et mutants revealed ET ‐specific differentially expressed genes and mostly independently characteristic, ET ‐specific differentially methylated regions. Loss of ET function results in pleiotropic developmental defects. The accumulation of cyclobutane pyrimidine dimers after ultraviolet stress in et mutants suggests an ET function in DNA repair.

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“…Unlike mammals, in which a global wave of demethylation occurs immediately after fertilization and then new m C marks are laid out, plants experience more local methylation reconfiguration in the early zygote [134,135]. DME supports temporally and spatially restricted expression of maternal origin alleles normally silenced in the rest of the plant and in other developmental phases, such as MEA, FLOWERING WAGENINGEN (FWA), FERTILIZATION INDEPENDENT SEED 2 (FIS2), or FLOWERING LOCUS C (FLC) in A. thaliana [88,[136][137][138][139]. DME also accounts for development-associated demethylation and activation of many mobile elements [140].…”

Section: Epigenetic Glycosylases the Plants' Unique Toolkitmentioning

confidence: 99%

Base Excision DNA Repair in Plants: Arabidopsis and Beyond

Grin,

Petrova,

Endutkin

et al. 2023

IJMS

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Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, E. coli, and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the Arabidopsis model, is important for future efforts to develop new crop varieties.

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Identification of putative Arabidopsis DEMETER target genes by GeneChip analysis

Cited by 10 publications

References 33 publications

<i>Hordeum vulgare</i> miežių lapų stabilių DNR baltymų kompleksų baltymų sudėties analizė

<i>Hordeum vulgare</i> miežių lapų stabilių DNR baltymų kompleksų baltymų sudėties analizė

EFFECTOR OF TRANSCRIPTION factors are novel plant‐specific regulators associated with genomic DNA methylation in Arabidopsis

Base Excision DNA Repair in Plants: Arabidopsis and Beyond

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