scholarly journals Contrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicolas Butel ◽  
Agnès Yu ◽  
Ivan Le Masson ◽  
Filipe Borges ◽  
Taline Elmayan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Host Plant ◽  
Transgene Silencing ◽  
Plant Genome ◽  
Plant Genomes ◽  
Epigenetic Control ◽  
Specific Attenuation ◽  
Endogenous Genes ◽  
Chromatin Modifying Complex

AbstractTransgenes that are stably expressed in plant genomes over many generations could be assumed to behave epigenetically the same as endogenous genes. Here, we report that whereas the histone H3K9me2 demethylase IBM1, but not the histone H3K4me3 demethylase JMJ14, counteracts DNA methylation of Arabidopsis endogenous genes, JMJ14, but not IBM1, counteracts DNA methylation of expressed transgenes. Additionally, JMJ14-mediated specific attenuation of transgene DNA methylation enhances the production of aberrant RNAs that readily induce systemic post-transcriptional transgene silencing (PTGS). Thus, the JMJ14 chromatin modifying complex maintains expressed transgenes in a probationary state of susceptibility to PTGS, suggesting that the host plant genome does not immediately accept expressed transgenes as being epigenetically the same as endogenous genes.

scholarly journals Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis transposons and gene regulatory regions

2017 ◽  
Author(s):  
Kyuha Choi ◽  
Xiaohui Zhao ◽  
Christophe Lambing ◽  
Charles J. Underwood ◽  
Thomas J. Hardcastle ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
Genome Instability ◽  
Nucleosome Occupancy ◽  
Plant Genome ◽  
Gene Promoters ◽  
Regulatory Regions ◽  
Plant Genomes ◽  
Meiotic Dsbs ◽  
Gene Regulatory

AbstractMeiotic recombination initiates via DNA double strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Recombination frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis SPO11-1-oligonucleotides. DSB hotspots occurred in gene promoters, terminators and introns, driven by AT-sequence richness, which excludes nucleosomes and allows SPO11-1 access. A strong positive relationship was observed between SPO11-1 DSBs and final crossover levels. Euchromatic marks promote recombination in fungi and mammals, and consistently we observe H3K4me3 enrichment in proximity to DSB hotspots at gene 5’-ends. Repetitive transposons are thought to be recombination-silenced during meiosis, in order to prevent non-allelic interactions and genome instability. Unexpectedly, we found strong DSB hotspots in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. Hotspot transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination-enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin on the DSB landscape. Epigenetic activation of transposon meiotic DSBs occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription and H3K4me3. Increased met1 SPO11-1 DSBs occurred most strongly within centromeres and Gypsy and CACTA/EnSpm coldspot transposons. Together, our work reveals complex interactions between chromatin and meiotic DSBs within genes and transposons, with significance for the diversity and evolution of plant genomes.

scholarly journals Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley

2021 ◽  
Vol 22 (13) ◽  
pp. 6783
Author(s):  
Renata Orłowska ◽  
Katarzyna A. Pachota ◽  
Wioletta M. Dynkowska ◽  
Agnieszka Niedziela ◽  
Piotr T. Bednarek
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Nuclear Dna ◽  
Point Mutations ◽  
Mobile Elements ◽  
Dna Demethylation ◽  
Plant Genome

A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.

High-throughput vectors for efficient gene silencing in plants

2002 ◽  
Vol 29 (10) ◽  
pp. 1217 ◽  
Author(s):  
Chris A. Helliwell ◽  
S. Varsha Wesley ◽  
Anna J. Wielopolska ◽  
Peter M. Waterhouse
Keyword(s):  
Gene Silencing ◽  
Insertional Mutagenesis ◽  
Single Step ◽  
Plant Genome ◽  
Specific Gene ◽  
Single Polymerase Chain Reaction ◽  
Efficient Gene ◽  
Gene Redundancy ◽  
Endogenous Genes ◽  
Rapid Generation

A major challenge in the post-genome era of plant biology is to determine the functions of all genes in the plant genome. A straightforward approach to this problem is to reduce or knockout expression of a gene with the hope of seeing a phenotype that is suggestive of its function. Insertional mutagenesis is a useful tool for this type of study but is limited by gene redundancy, lethal knockouts, non-tagged mutants, and the inability to target the inserted element to a specific gene. The efficacy of gene silencing in plants using inverted-repeat transgene constructs that encode a hairpin RNA (hpRNA) has been demonstrated by a number of groups, and has several advantages over insertional mutagenesis. In this paper we describe two improved pHellsgate vectors that facilitate rapid generation of hpRNA-encoding constructs. pHellsgate 4 allows the production of an hpRNA construct in a single step from a single polymerase chain reaction product, while pHellsgate 8 requires a two-step process via an intermediate vector. We show that these vectors are effective at silencing three endogenous genes in Arabidopsis, FLOWERING LOCUS C, PHYTOENE DESATURASE and ETHYLENE INSENSITIVE 2. We also show that a construct of sequences from two genes silences both genes.

scholarly journals RNA directed DNA methylation and seed plant genome evolution

2020 ◽  
Vol 39 (8) ◽  
pp. 983-996
Author(s):  
R. Wambui Mbichi ◽  
Qing-Feng Wang ◽  
Tao Wan
Keyword(s):  
Dna Methylation ◽  
Genome Evolution ◽  
Plant Genome ◽  
Seed Plant ◽  
Plant Genome Evolution

scholarly journals H3 Lysine 9 Methylation Is Maintained on a Transcribed Inverted Repeat by Combined Action of SUVH6 and SUVH4 Methyltransferases

2005 ◽  
Vol 25 (23) ◽  
pp. 10507-10515 ◽  
Author(s):  
Michelle L. Ebbs ◽  
Lisa Bartee ◽  
Judith Bender
Keyword(s):  
Dna Methylation ◽  
Chromatin Immunoprecipitation ◽  
Inverted Repeat ◽  
Histone H3 ◽  
Inverted Repeats ◽  
Chromatin Modifications ◽  
Double Stranded Rna ◽  
Repeat Sequences ◽  
Endogenous Genes ◽  
Combined Action

ABSTRACT Transcribed inverted repeats are potent triggers for RNA interference and RNA-directed DNA methylation in plants through the production of double-stranded RNA (dsRNA). For example, a transcribed inverted repeat of endogenous genes in Arabidopsis thaliana, PAI1-PAI4, guides methylation of itself as well as two unlinked duplicated PAI genes, PAI2 and PAI3. In previous work, we found that mutations in the SUVH4/KYP histone H3 lysine 9 (H3 K9) methyltransferase cause a loss of DNA methylation on PAI2 and PAI3, but not on the inverted repeat. Here we use chromatin immunoprecipitation analysis to show that the transcribed inverted repeat carries H3 K9 methylation, which is maintained even in an suvh4 mutant. PAI1-PAI4 H3 K9 methylation and DNA methylation are also maintained in an suvh6 mutant, which is defective for a gene closely related to SUVH4. However, both epigenetic modifications are reduced at this locus in an suvh4 suvh6 double mutant. In contrast, SUVH6 does not play a significant role in maintenance of H3 K9 or DNA methylation on PAI2, transposon sequences, or centromere repeat sequences. Thus, SUVH6 is preferentially active at a dsRNA source locus versus targets for RNA-directed chromatin modifications.

TEMPERATURE-SENSITIVE NODULATION AND N2 FIXATION OF Rhizobium leguminosarum BIOVAR Phaseoli STRAINS

1986 ◽  
Vol 66 (2) ◽  
pp. 217-224 ◽  
Author(s):  
R. J. RENNIE ◽  
G. A. KEMP
Keyword(s):  
Host Plant ◽  
Temperature Regime ◽  
Rhizobium Leguminosarum ◽  
Spontaneous Mutation ◽  
Plant Genome ◽  
Prolonged Storage ◽  
Field Bean ◽  
Temperature Sensitive ◽  
Culture Collections ◽  
Symbiotic Properties

Two strains of Rhizobium leguminosarum biovar phaseoli, both previously Nod+Fix+ and efficient in N2 fixation, now have altered symbiotic properties presumably through spontaneous mutation. Rhizobium leguminosarum biovar phaseoli strain RCR 3605 was Nod−Fix− in a cool growth temperature regime (14–23 °C) and Nod+Fix− in a warm regime (17–23 °C) on seven of nine bean cultivars studied. Rhizobium leguminosarum biovar phaseoli strain CIAT 57 was Nod+Fix− in both temperature regimes. CIAT 57 and RCR 3605 are synonyms for strains derived from the same parent strain but housed in different culture collections. The nodulation deficiency in CIAT 57 is presumably genetically predetermined in the bacterium rather than in the plant because no Nod+Fix+ phenotype was identified on nine bean cultivars tested. A control R. leguminosarum biovar phaseoli strain, RCR 3644, was efficient on all cultivars. In the warm temperature regime, the Nod+Fix− phenotype was observed with strain RCR 3605 only on some cultivars, suggesting that the host plant genome played a role in this ineffective symbiosis. It is likely that deleterious genetic mutations during prolonged storage may be altering the N2-fixing ability of these rhizobial strains and that commercial inoculants must be continually monitored for symbiotic performance of strains with a variety of host plant cultivars. Key words: Field bean, Rhizobium leguminosarum biovar phaseoli, N2 fixation

scholarly journals Epigenetic Control of Angiogenesis via DNA Methylation

Circulation ◽  
2011 ◽  
Vol 123 (25) ◽  
pp. 2916-2918 ◽  
Author(s):  
Marcus P. Cooper ◽  
John F. Keaney
Keyword(s):  
Dna Methylation ◽  
Epigenetic Control

scholarly journals DNA methylation and epigenetic control of cellular differentiation

Cell Cycle ◽  
2010 ◽  
Vol 9 (19) ◽  
pp. 3880-3883 ◽  
Author(s):  
David A. Khavari ◽  
George L. Sen ◽  
John L. Rinn
Keyword(s):  
Dna Methylation ◽  
Cellular Differentiation ◽  
Epigenetic Control

scholarly journals Screening for Compounds That Modulate Epigenetic Regulation of the Transcriptome

2011 ◽  
Vol 16 (10) ◽  
pp. 1137-1152 ◽  
Author(s):  
Richard M. Eglen ◽  
Terry Reisine
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Posttranslational Modifications ◽  
High Throughput Screening ◽  
Dna Methyltransferases ◽  
Methylation Pattern ◽  
Gene Activity ◽  
Epigenetic Control ◽  
Dnmt Inhibitors ◽  
Inhibit Gene Expression

Epigenetic control of the transciptome is a complex and highly coordinated cellular process. One critical mechanism involves DNA methylation, mediated by distinct but related DNA methyltransferases (DNMTs). Although several DNMT inhibitors are available, most are nonselective; selective DNMT inhibitors, therefore, could be optimal as therapeutics, as well acting as chemical probes to elucidate the fundamental biology of individual DNMTs. DNA methylation is a stable chemical modification, yet posttranslational modification of histones is transitory, with reversible effects on gene expression. Histone posttranslational modifications influence access of transcription factors to DNA target sites to affect gene activity. Histones are regulated by several enzymes, including acetylases (HATs), deacetylases (HDACs), methyltransferases (HMTs), and demethylases (HDMTs). Generally, HATs activate, whereas HDACs suppress gene activity. Specifically, HMTs and HDMTs can either activate or inhibit gene expression, depending on the site and extent of the methylation pattern. There is growing interest in drugs that target enzymes involved in epigenetic control. Currently, a range of high-throughput screening (HTS) technologies are used to identify selective compounds against these enzymes. This review focuses on the rationale for drug development of these enzymes, as well the utility of HTS methods used in identifying and optimizing novel selective compounds that modulate epigenetic control of the human transcriptome.

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