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| Status |
Public on Apr 25, 2023 |
| Title |
RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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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| Overall design |
RNA degradome analysis (ATH1036-41; ATH1082-87): Comparing the RNA decay profiles allowed for the detection of abundant monophosphorylated 5' ends (5'P) within transcripts in xrn4 that were absent in dne1xrn4. Thereby, we identified a number of 5'P sites that were dependent on DNE1 activity.
RNA-seq analysis (ATH1046-57): For comparing full-length transcript abundances between xrn4 and dne1xrn4.
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| Contributor(s) |
Nagarajan VK, Green PJ |
| Citation(s) |
37070465 |
| Submission date |
Jan 07, 2022 |
| Last update date |
Apr 25, 2023 |
| Contact name |
Pamela J Green |
| E-mail(s) |
green@dbi.udel.edu
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| Organization name |
Delaware Biotechnology Institute
|
| Department |
Plant and Soil Sciences
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| Street address |
15 Innovation Way
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19711 |
| Country |
USA |
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| Platforms (2) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
| GPL24270 |
NextSeq 550 (Arabidopsis thaliana) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA795486 |
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