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| Status |
Public on Oct 31, 2015 |
| Title |
Chemical modifications mark alternatively spliced and actively degrading messenger RNAs in Arabidopsis and humans |
| Organisms |
Arabidopsis thaliana; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Other
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| Summary |
Post-transcriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as transfer RNAs (tRNAs), growing evidence indicates that messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) are likewise modified. Here, we apply our High-throughput Annotation of Modified Ribonucleotides (HAMR) pipeline to identify and classify modifications that affect Watson-Crick base-pairing at three different levels of the human and Arabidopsis thaliana transcriptomes (polyadenylated, small, and degrading RNAs). We find modifications primarily within actively degrading mRNAs and lncRNAs, suggesting they can act as a potent signal for RNA turnover. Additionally, modifications within stable mRNAs mark alternatively spliced introns, suggesting they regulate splicing. Furthermore, these modifications target mRNAs with coherent functions, including stress responses. Thus, our comprehensive analysis of RNA modification across multiple RNA classes yields new functional insights into these covalent RNA additions.
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| Overall design |
polyA-selected RNA-seq, smRNA-seq, and polyA-selected global mapping of uncapped transcripts (GMUCT) in Arabidopsis thaliana; smRNA-seq in HEK293T and HeLa human cell lines.
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| Contributor(s) |
Vandivier LE, Campos R, Kuksa PP, Silverman IM, Wang L, Gregory BD |
| Citation(s) |
26561561 |
| Submission date |
Feb 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lee Elliott Vandivier |
| E-mail(s) |
lee.vandivier@gmail.com
|
| Organization name |
University of Pennsylvania
|
| Street address |
433 S. University Ave Rm 104
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA276134 |
| SRA |
SRP055443 |
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