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Arabidopsis thaliana

ABSTRACT: Genome-wide mapping of uncapped and cleaved transcripts reveals a role for the nuclear messenger RNA cap-binding complex in plant co-translational RNA decay

PROVIDER: PRJNA292441 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2153780.fastq.gz	Fastqsanger.gz
	SRR2153781.fastq.gz	Fastqsanger.gz
	SRR2921867.fastq.gz	Fastqsanger.gz
	SRR2921868.fastq.gz	Fastqsanger.gz

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Genome-wide mapping of uncapped and cleaved transcripts reveals a role for the nuclear messenger RNA cap-binding complex in plant co-translational RNA decay

Project description:RNA turnover is necessary for controlling proper mRNA levels post-transcriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5’ end to the 3’ end, such as XRN4, or in the opposite direction by the multi-subunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of co-translational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of co-translational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that co-translational RNA decay is XRN4-dependent. Additionally, studies in plants lacking CAP-BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap-binding complex, reveal a role for this protein in co-translational decay. In total, our results demonstrate the global prevalence and features of co-translational RNA decay in a plant transcriptome.

2016-09-30 | GSE71913 | GEO

RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis

Project description:To gain insight into the functional role of DNE1 in cytoplasmic mRNA decay, we performed Parallel Analysis of RNA Ends (PARE) and Global Mapping of Uncapped and Cleaved Transcripts (GMUCT) analysis to identify DNE1-dependent cleavage sites based on their sensitivity to XRN4 within the Arabidopsis transcriptome

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PELOTA and HBS1 suppress co-translational messenger RNA decay in Arabidopsis

Project description:PELOTA and HBS1 suppress co-translational messenger RNA decay in Arabidopsis

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PELOTA and HBS1 suppress co-translational messenger RNA decay in Arabidopsis [GMUCT]

Project description:PELOTA and HBS1 suppress co-translational messenger RNA decay in Arabidopsis [GMUCT]

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Systematic discovery of cap-independent translation sequences in human and viral genomes

Project description:To investigate gene specificity at the level of translation in both the human genome and viruses, we devised a high-throughput bicistronic assay to quantify cap-independent translation. We uncovered thousands of novel cap-independent translation sequences, and we provide insights on the landscape of translational regulation in both humans and viruses. We find extensive translational elements in the 3′ untranslated region of human transcripts and the polyprotein region of uncapped RNA viruses. Through the characterization of regulatory elements underlying cap-independent translation activity, we identify potential mechanisms of secondary structure, short sequence motif,and base pairing with the 18S ribosomal RNA (rRNA). Furthermore, we systematically map the 18S rRNA regions for which reverse complementarity enhances translation. Thus, we make available insights into the mechanisms of translational control in humans and viruses.

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Characterization of human malaria parasite Plasmodium falciparum eIF4E homologue and mRNA 5â² cap status

Project description:The mRNA 5â² cap is normally essential for eukaryotic mRNA translation, stabilization and transport and both the cap and eIF4E are important elements of post-transcriptional gene regulation. To further our understanding of mRNA translation in the human malaria parasite Plasmodium falciparum, we have investigated the parasite translation initiation factor eIF4E and its interaction with 5â² capped mRNA. We have purified P. falciparum eIF4E as a recombinant protein and demonstrated that it has canonical mRNA 5â² cap binding activity. We used this protein to purify P. falciparum full-length 5â² capped mRNAs from total parasite RNA. Microarray analysis comparing total and eIF4E-purified 5â² capped mRNAs shows that a subset of 34 features were more than two-fold under-represented in the purified RNA sample, including 19 features representative of nuclear transcripts. The uncapped nuclear transcripts may represent a class of mRNAs targeted for storage and cap removal. Keywords: total RNA vs purified capped mRNA The microarray data were obtained from four hybridizations using RNA from two independent GST-PfeIF4E purifications from separate malaria cultures.

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CEG1 DEPLETION REVEALS MECHANISMS GOVERNING DEGRADATION OF NON-CAPPED RNAs

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Project description:In order to gain insight into relative stability of transcripts in plants that lacked m6A, we performed global mapping of uncapped and cleaved transcripts

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PELOTA and HBS1 suppress co-translational messenger RNA decay in Arabidopsis [mRNA-Seq]

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Regulatory and evolutionary footprints of messenger RNA secondary structure in primate transcriptomes

Project description:Messenger RNA secondary structure is critical to all aspects of post-transcriptional regulation. However, the global regulatory and evolutionary significance of mRNA secondary structure remains largely illusive. Here, we describe a transcriptome-wide analysis of RNA secondary structure in humans and two non-human primates, based on a high-throughput, nuclease-mediated, structure mapping approach. Using this methodology, we uncover global patterns of mRNA secondary structure, which we find to be conserved through primate evolution. We provide evidence for secondary structure-based regulatory pathways, which impact on gene expression through associations with translational machinery and RNA-binding proteins, including components of the microprocessor complex. Our results lend support to an unexpected, conserved mechanism by which highly structured regions of mRNAs serve as processing sites for small RNAs, resulting in subsequent turnover. Global mRNA secondary structure analysis in primate transcriptomes using high-throughput, nuclease-mediated, structure mappinng approaches of dsRNA-seq and ssRNA-seq, also with polyA+ mRNA-seq, smRNA-seq (small RNA), and genome-wide mapping of uncapped and cleaved transcripts (GMUCT); these NGS-seq experiments were carried out in three primate brains as well as three different cell lines, both in in vitro and in vivo.

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