Global analysis of siRNA‐mediated transcriptional gene silencing

Kavi, Harsh H.; Xie, Weiwu; Fernandez, Harvey R.; Birchler, James A.

doi:10.1002/bies.20328

Cited by 10 publications

(9 citation statements)

References 17 publications

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“…In the classic model, and similarly as in mammalian cells, plant telomeres were viewed as heterochromatic loci (27). A more recent study, however, characterized A. thaliana telomeric chromatin as an intermediate heterochromatin possessing both hetero- and euchromatin-specific histone modifications (8).…”

Section: Introductionmentioning

confidence: 99%

Compromised telomere maintenance in hypomethylated Arabidopsis thaliana plants

Ogrocká¹,

Polanská²,

Majerová³

et al. 2013

Nucleic Acids Research

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Telomeres, nucleoprotein structures at the ends of linear eukaryotic chromosomes, are important for the maintenance of genomic stability. Telomeres were considered as typical heterochromatic regions, but in light of recent results, this view should be reconsidered. Asymmetrically located cytosines in plant telomeric DNA repeats may be substrates for a DNA methyltransferase enzyme and indeed, it was shown that these repeats are methylated. Here, we analyse the methylation of telomeric cytosines and the length of telomeres in Arabidopsis thaliana methylation mutants (met 1-3 and ddm 1-8), and in their wild-type siblings that were germinated in the presence of hypomethylation drugs. Our results show that cytosine methylation in telomeric repeats depends on the activity of MET1 and DDM1 enzymes. Significantly shortened telomeres occur in later generations of methylation mutants as well as in plants germinated in the presence of hypomethylation drugs, and this phenotype is stably transmitted to the next plant generation. A possible role of compromised in vivo telomerase action in the observed telomere shortening is hypothesized based on telomere analysis of hypomethylated telomerase knockout plants. Results are discussed in connection with previous data in this field obtained using different model systems.

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Section: Introductionmentioning

confidence: 99%

Compromised telomere maintenance in hypomethylated Arabidopsis thaliana plants

Ogrocká¹,

Polanská²,

Majerová³

et al. 2013

Nucleic Acids Research

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“…More and more evidence has shown that gene silencing is widely adopted in plant immunity. In the past, studies often focused on transposon or siRNA-mediated RNA silence [5,6] . Since miRNAs and siRNAs share many features in common, it is supposed that miRNAs may also be involved in silencing invaders.…”

Section: Introductionmentioning

confidence: 99%

High GC content: Critical parameter for predicting stress regulated miRNAs in Arabidopsis thaliana

Mishra

Agarwal²,

Jain³

et al. 2009

Bioinformation

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Plants like Arabidopsis thaliana are convenient model systems to study fundamental questions related to regulation of the stress transcriptome in response to stress challenges. Microarray results of the Arabidopsis transcriptome indicate that several genes could be upregulated during multiple stresses. High-salinity, drought, and low temperature are three common environmental stress factors that seriously influence plant growth and development worldwide. Recently, microRNAs (miRNAs) have emerged as a class of gene expression regulators that have also been linked to stress responses. However, the relationship between miRNA expression and stress responses is just beginning to be explored. Here we have computationally analyzed 123 non redundant miRNA sequences reported for Arabidopsis thaliana, including 17 miRNA sequences which were reported to be stress regulated in literature. A significant increase in the GC content of stress regulated miRNA sequences was observed which further extends the view that miRNAs act as ubiquitous regulators under stress conditions. GC content may also be considered as a critical parameter for predicting stress regulated miRNAs in plants like Arabidopsis thaliana.

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“…Control shRNA contained the same base composition as IE-3 specific RNAs but the base sequence was scrambled. This inhibitory RNA is therefore initially expressed as shRNA but is then processed by the enzyme Dicer into siRNA which is the active component in the RNA induced silencing complex (RISC) [40]. The transfection efficiency of IE-3 specific fluorescently labeled siRNAs or GFP reporter plasmids into the murine bone marrow stromal cell line M2-10B4 was 70-80% (not shown).…”

Section: Resultsmentioning

confidence: 99%

The effect of murine cytomegalovirus IE-3 specific shRNA is dependent on intragenic target site due to multiple transcription initiation sites

2011

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BackgroundMurine cytomegalovirus (MCMV) is closely related to human cytomegalovirus (HCMV) which is responsible for a variety of diseases, including retinitis, in immunocompromised individuals. Small inhibitory RNA molecules directed against essential viral regulatory genes may prove clinically useful.MethodsSmall hairpin RNAs (shRNAs) directed against the essential MCMV immediate early-3 gene (IE-3) were designed and tested in vitro at m.o.i.'s of 2 and 0.2 to determine if virus replication could be inhibited.ResultsAt m.o.i. = 2, a MCMV IE-3 specific shRNA specific for sequences at the beginning of exon 5 inhibited virus replication with a maximum decrease in virus titer of approximately two logs at day 5 p.i. Surprisingly, however, at m.o.i. = 0.2, the same shRNA enhanced virus replication. In the latter case, the main IE-3 product observed in infected cells was not the expected 88 kd full length IE-3 protein observed at high m.o.i. but rather a truncated 45 kd form of this protein. Rapid analysis of 5' cDNA ends (5' RACE) indicated that substantial differences exist in the transcript profile produced by the IE-3 gene at low and high m.o.i. early after infection and that multiple transcripts are produced under both conditions. One such transcript, which originated in exon 5 of the IE-3 gene, was located outside the region targeted by our shRNA and was the major transcript produced at low m.o.i. Targeting of this exon 5 transcript with a second shRNA resulted in inhibition of virus replication at both low and high m.o.i.ConclusionsThese studies indicate that IE-3 has a complex transcriptional profile and that shRNA targeting of this and other viral regulatory genes which produce multiple transcripts may have unexpected effects on virus replication.

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Global analysis of siRNA‐mediated transcriptional gene silencing

Cited by 10 publications

References 17 publications

Compromised telomere maintenance in hypomethylated Arabidopsis thaliana plants

Compromised telomere maintenance in hypomethylated Arabidopsis thaliana plants

High GC content: Critical parameter for predicting stress regulated miRNAs in Arabidopsis thaliana

The effect of murine cytomegalovirus IE-3 specific shRNA is dependent on intragenic target site due to multiple transcription initiation sites

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