A 3600-bp RNA-directed RNA polymerase (RdRP)–specific cDNA comprising an open reading frame (ORF) of 1114 amino acids was isolated from tomato. The putative protein encoded by this ORF does not share homology with any characterized proteins. Antibodies that were raised against synthetic peptides whose sequences have been deduced the shown to specifically detect 127-kD tomato RdRP protein. immunoresponse antibodies correlated enzymatic activity profile after chromatography on Q-, poly(A)–,...

Significance Similar to changes in DNA sequence, induced or naturally occurring variation cytosine methylation can impact gene expression. How distinct states of genes and transposons, called epialleles, emerge is not well understood. Here, we report that combining identical genomes with drastically different patterns the same individual results an epigenomic shock characterized by widespread Many novel epialleles found parents are formed at whereas transposons often experience decreased...

Abstract In flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of linker H1, and specific epigenetic modifications, such as high DNA methylation at both CG non-CG sites. How H2A.W regulates organization interacts with other heterochromatic features unclear. Here, we create a h2a.w null mutant via CRISPR-Cas9, h2a.w-2 , to analyze in vivo function H2A.W. We find that antagonizes deposition H1 accessibility are moderately decreased heterochromatin....

Previous analysis of potato spindle tuber viroid (PSTVd) RNA-infected tobacco plants has suggested that an RNA-DNA interaction could trigger de novo methylation PSTVd transgene sequences. Using the genomic sequencing technique, pattern associated with RNA-directed DNA process been characterized. Three different constructs all showed a similar methylation. Most cytosines at symmetrical as well non-symmetrical positions appeared to be methylated in both strands Heavy was mostly restricted cDNA...

Abstract Background Phosphorylation of eIF2α provides a key mechanism for down-regulating protein synthesis in response to nutrient starvation or stresses mammalian and yeast cells. However, this process has not been well characterized plants Results We show here that amino acid purine starvations, UV, cold shock wounding, the Arabidopsis GCN2 kinase (AtGCN2) is activated phosphorylates eIF2α. AtGCN2 essential plant growth stress situations its activity results strong reduction global...

In higher plants, RNA–DNA interactions can trigger de novo methylation of genomic sequences via a process that is termed RNA-directed DNA (RdDM). potato spindle tuber viroid (PSTVd)-infected tobacco this potentially lead to all C residues at symmetrical and nonsymmetrical sites within chromosomal inserts consist multimers the 359-bp-long PSTVd cDNA. Using cDNA subfragments, we found targets with as few 30 nt sequence complementarity RNA are detected methylated. Genomic sequencing analyses...

AbstractSINEs (short interspersed elements) are an abundant class of transposable elements found in a wide variety eukaryotes. Using the genomic sequencing technique, we observed that plant S1 SINE retroposons mainly integrate hypomethylated DNA regions and targeted by methylases. Methylation can then spread from into flanking sequences, creating distal epigenetic modifications. This methylation spreading is vectorially directed upstream or downstream element, suggesting it could be...

Summary Viroid infection is associated with the production of short interfering RNAs (siRNAs), a hallmark post‐transcriptional gene silencing (PTGS). However, viroid autonomously replicating in nucleus have not been shown to trigger degradation homologous RNA cytoplasm. To investigate potential viroids for induction silencing, non‐infectious fragments potato spindle tuber (PSTVd) cDNA were transcriptionally fused 3′ end green fluorescent protein (GFP)‐coding region. Introduction such...

Biogenesis of the vast majority plant siRNAs depends on activity plant-specific RNA polymerase IV (PolIV) enzyme. As part RNA-dependent DNA methylation (RdDM) process, PolIV-dependent (p4-siRNAs) are loaded onto an ARGONAUTE4-containing complex and guide de novo methyltransferases to target loci. Here we show that double-stranded binding proteins DRB2 DRB4 required for proper accumulation p4-siRNAs. In flowers, loss results in increased p4-siRNAs but not ta-siRNAs, inverted repeat...

Abstract Transposable elements (TEs) are prevalent in most eukaryotes, and host genomes have devised silencing strategies to rein TE activity. One of these, transcriptional silencing, is generally associated with DNA methylation short interfering RNAs. Here we show that the Arabidopsis genes MAIL1 MAIN define an alternative pathway independent Mutants for or exhibit release appear impaired condensation pericentromeric heterochromatin. Phylogenetic analysis suggests not only encode a...

We have characterized the two families of SINE retroposons present in Arabidopsis thaliana. The origin, distribution, organization, and evolutionary history RAthE1 RAthE2 elements were studied compared to well-characterized S1 element from Brassica. Our studies show that RAthE1, RAthE2, generated independently three different tRNAs. are older than family all tested Cruciferae species. is unusual for SINEs. 144 genome cannot be classified distinct subfamilies ages as case S1, mammalian...

The proper temporal and spatial expression of genes during plant development is governed, in part, by the regulatory activities various types small RNAs produced different RNAi pathways. Here we report that transgenic Arabidopsis plants constitutively expressing rapeseed SB1 SINE retroposon exhibit developmental defects resembling those observed some mutants. We show RNA interacts with HYL1 (DRB1), a double-stranded RNA-binding protein (dsRBP) associates Dicer homologue DCL1 to produce...

Nanoviruses, multicomponent single-stranded DNA plant viruses, encode a unique cell cycle link protein, Clink, that interacts with retinoblastoma-related proteins (RBR). We have established transgenic Arabidopsis thaliana lines conditionally express Clink or variant deficient in RBR binding. By controlled induction of expression, we demonstrated the capacity protein to alter function vivo. showed transcription both S-phase-specific and G2/M-phase-specific genes was up-regulated depending on...

Abstract Background Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During replication, both genetic information chromatin modifications must be faithfully passed on daughter strands. There evidence that polymerases play a role in silencing, but extent their contribution how it relates heterochromatin maintenance...

Transcription is an important control point in the transposable element mobilization process. To better understand regulation of plant SINE (Short Interspersed Elements) S1, its promoter sequence was studied using vitro pol III transcription system derived from tobacco cells. We show that internal S1 can be functional although upstream external sequences were found to enhance this basal level transcription. For one putative 'master' locus (na7), three CAA triplets (in positions -12, -7 and...

Constitutive heterochromatin is associated with repressive epigenetic modifications of histones and DNA which silence transcription. Yet, particular mutations or environmental changes can destabilize heterochromatin-associated silencing without noticeable in marks. Factors allowing transcription this nonpermissive chromatin context remain poorly known. Here, we show that the factor IIH component UVH6 mediator subunit MED14 are both required for heat stress-induced transcriptional release...

In plants and animals, a large number of double-stranded RNA binding proteins (DRBs) have been shown to act as non-catalytic cofactors DICERs participate in the biogenesis small RNAs involved silencing. We previously that loss Arabidopsis thaliana's DRB2 protein results significant increase population polymerase IV (p4) dependent siRNAs, which are RNA-directed DNA methylation (RdDM) process. Surprisingly, despite this observation, we show work is part high molecular weight complex does not...

A strategy based on random PCR amplification was used to isolate new repetitive elements of Arabidopsis thaliana . One the product analyzed by this approach contained a tandem minisatellite sequence composed 33 bp repeated units. The genomic locus corresponding isolated screening lambda library. New related loci were also from library with 14 mer oligonucleotide representing region conserved among different Alignment consensus for each allowed definition an core that shows strong...

Despite the ubiquitous distribution of tRNA-related short interspersed elements (SINEs) in eukaryotic species, very little is known about synthesis and processing their RNAs. In this work, we have characterized detail different RNA populations resulting from expression a SINE S1 founder copy Arabidopsis thaliana . The main population composed poly(A)-ending (pa) RNAs, while two minor correspond to full-length (fl) or poly(A) minus [small cytoplasmic (sc)] Part RNAs modified by 3′-terminal...

Summary The two paralogous Arabidopsis genes MAINTENANCE OF MERISTEMS (MAIN) and LIKE1 (MAIL1) encode a conserved retrotransposon‐related plant mobile domain are known to be required for silencing of transposable elements (TE) primary root development. Loss function either MAIN or MAIL1 leads release heterochromatic TEs, reduced condensation pericentromeric heterochromatin, cell death meristem cells growth arrest the soon after germination. Here, we show that they act in one protein complex...

<i>Brassica oleracea</i> and <i>Arabidopsis thaliana</i> belong to the <i>Brassicaceae</i><i>(Cruciferae)</i> family diverged 16 19 million years ago. Although genome size of <i>B. (∼600 base pairs) is more than four times that <i>A. (∼130 pairs), their gene content believed be very similar with 85% sequence identity in coding region. Therefore, this important difference likely reflect a different rate non-coding DNA accumulation....