RNA degradome--its biogenesis and functions

Jackowiak, Paulina; Nowacka, Martyna; Strozycki, Pawel M.; Figlerowicz, Marek

doi:10.1093/nar/gkr450

Cited by 52 publications

(42 citation statements)

References 82 publications

(185 reference statements)

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“…These small RNAs control essential cellular processes by regulating development and homeostasis and defending against retrotransposons and viral infections (Johnson and Sundaresan 2007; Bonnet et al 2006). It has become increasingly evident that the range of known, potentially functional, non-coding RNAs is likely to expand and includes RNA degradation intermediates that have not been considered so far (Jackowiak et al 2011). RNA degradation is a highly efficient process that is associated with RNA maturation, quality control and turnover.…”

Section: Introductionmentioning

confidence: 99%

Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions

et al. 2013

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It is becoming increasingly evident that the RNA degradome is a crucial component of the total cellular RNA pool. Here, we present an analysis of the medium-sized RNAs (midi RNAs) that form in Arabidopsis thaliana. Our analyses revealed that the midi RNA fraction contained mostly 20–70-nt-long fragments derived from various RNA species, including tRNA, rRNA, mRNA and snRNA. The majority of these fragments could be classified as stable RNA degradation intermediates (RNA degradants). Using two dimensional polyacrylamide gel electrophoresis, we demonstrated that high copy number RNA (hcn RNA) degradants appear in plant cells not only during stress, as it was earlier suggested. They are continuously produced also under physiological conditions. The data collected indicated that the accumulation pattern of the hcn RNA degradants is organ-specific and can be affected by various endogenous and exogenous factors. In addition, we demonstrated that selected degradants efficiently inhibit translation in vitro. Thus, the results of our studies suggest that hcn RNA degradants are likely to be involved in the regulation of gene expression in plants.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-013-0079-3) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions

et al. 2013

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“…The amount of mRNA that can be isolated from a cell is small, and amplification steps are necessary prior to sequencing. RNA is also less stable than DNA, starting to degrade quite quickly when a cell dies, being destroyed by the still active RNAses in the cell (Jackowiak et al 2011). Therefore, the lysis protocol has to be adjusted in order to break the cell without destroying the RNA.…”

Section: Single-cell Transcriptomicsmentioning

confidence: 99%

Exploring the oceanic microeukaryotic interactome with metaomics approaches

Krabberød¹,

Bjorbækmo²,

Shalchian-Tabrizi³

et al. 2017

Aquat. Microb. Ecol.

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THE MICROBIAL OCEANOur collective awareness of the significance of marine ecosystems has increased steadily during the last 40 yr, progressing in concert with the development of new technologies that have allowed us to dig deeper into the microbial world. A number of key events can be identified from this period, for example the formulation of the microbial-loop concept, the discovery of abundant photoautotrophic (Synechococcus and Prochlorococcus) and heterotrophic (SAR11) pico-sized prokaryotic plankton as well as novel lineages of heterotrophic picoeukaryotes (e.g. MALV and MAST), the recognition of the importance of Archaea in oceanic plankton, the realization that the majority of marine microbes cannot be cultured, the discovery of the rare biosphere and the key role of viruses in oceanic communities (Kirchman 2008 ABSTRACT: Biological communities are systems composed of many interacting parts (species, populations or single cells) that in combination constitute the functional basis of the biosphere. Animal and plant ecologists have advanced substantially our understanding of ecological interactions. In contrast, our knowledge of ecological interaction in microbes is still rudimentary. This represents a major knowledge gap, as microbes are key players in almost all ecosystems, particularly in the oceans. Several studies still pool together widely different marine microbes into broad functional categories (e.g. grazers) and therefore overlook fine-grained species/population-specific interactions. Increasing our understanding of ecological interactions is particularly needed for oceanic microeukaryotes, which include a large diversity of poorly understood symbiotic relationships that range from mutualistic to parasitic. The reason for the current state of affairs is that determining ecological interactions between microbes has proven to be highly challenging. However, recent technological developments in genomics and transcriptomics (metaomics for short), coupled with microfluidics and high-performance computing are making it increasingly feasible to determine ecological interactions at the microscale. Here, we present our views on how this field will advance thanks to the progress in metaomics approaches as well as potential avenues for future research.

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“…910 But in comparison with DNA, RNA molecules are far more easily degraded because of widely distribution of ribonuclease(RNnas) enzyme in environment. 11 Saverio Giapaoli et al 12 reported forFLUID kit testing results from eight laboratories for identification of vaginal fluids by analyzing the commensal bacteria genomes. The multiplex realtime PCR was used to probe genomic DNA from six microbes.…”

Section: Introductionmentioning

confidence: 99%