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Decapped mRNAs during Arabidopsis Early Flower Development

ABSTRACT: The composition of the transcriptome is regulated by both mRNA synthesis and degradation. One route for mRNA decay is through 5’ decapping, which can be initiated by decapping enzymes and small RNAs. Although decapped RNAs are an important intermediate for mRNA decay, their identity and abundance have never been studied on a large scale. Here we present an experimental method for transcriptome-wide profiling of decapped mRNAs. We applied the method to study the prevalence of decapped transcripts during the early stages of Arabidopsis thaliana flower development. Decapped transcripts were identified for the majority of expressed genes, although at different levels. By comparing decapped RNA levels with steady-state overall transcript levels, our study provides evidence for widespread decapping-mediated mRNA degradation control in numerous biological processes and for genes of varied molecular functions, implying that mRNA decapping is a dynamically regulated process. Sequence analyses identified structural features of transcripts and cis-elements that were associated with levels of decapping.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE12043 | GEO | 2008/10/10

SECONDARY ACCESSION(S): PRJNA113369

REPOSITORIES: GEO

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Project description:LlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case1 Three putative effects of the asRNAs were considered in this study: in case 1 (this model) , the binding of the asRNA to the corresponding mRNA induces degradation of the duplex. In case 2, the binding of the asRNA to the mRNA induces degradation of the mRNA, but not of the asRNA. In case 3, the mRNA and the asRNA bind reversibly to form a stable duplex, preventing translation of the mRNA. In all the three cases, binding to the ribosome protects the mRNA from the effect of the asRNA. This model is described in the article: Bacterial antisense RNAs are mainly the product of transcriptional noise. Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M. Sci Adv 2016 Mar; 2(3): e1501363 Abstract: cis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing nine different asRNAs in Mycoplasma pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome. This model is hosted on BioModels Database and identified by: MODEL1511170000. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Decapped mRNAs during Arabidopsis Early Flower Development

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