The role of the 5′-3′ exoribonuclease XRNA in transcriptome-wide mRNA degradation
The steady-state level of each mRNA in a cell is a balance between synthesis and degradation. Here, we use high-throughput RNA sequencing (RNASeq) to determine the relationship between mRNA degradation and mRNA abundance on a transcriptome-wide scale. The model organism used was the bloodstream form...
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| Main Authors: | , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
September 26, 2011
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| In: |
RNA
Year: 2011, Volume: 17, Issue: 11, Pages: 2039-2047 |
| ISSN: | 1469-9001 |
| DOI: | 10.1261/rna.2837311 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1261/rna.2837311 Verlag, lizenzpflichtig, Volltext: http://rnajournal.cshlp.org/content/17/11/2039 
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| Author Notes: | Theresa Manful, Abeer Fadda, and Christine Clayton |
| Summary: | The steady-state level of each mRNA in a cell is a balance between synthesis and degradation. Here, we use high-throughput RNA sequencing (RNASeq) to determine the relationship between mRNA degradation and mRNA abundance on a transcriptome-wide scale. The model organism used was the bloodstream form of Trypanosoma brucei, a protist that lacks regulation of RNA polymerase II initiation. The mRNA half-lives varied over two orders of magnitude, with a median half-life of 13 min for total (rRNA-depleted) mRNA. Data for poly(A)+ RNA yielded shorter half-lives than for total RNA, indicating that removal of the poly(A) tail was usually the first step in degradation. Depletion of the major 5′-3′ exoribonuclease, XRNA, resulted in the stabilization of most mRNAs with half-lives under 30 min. Thus, on a transcriptome-wide scale, degradation of most mRNAs is initiated by deadenylation. Trypanosome mRNA levels are strongly influenced by gene copy number and mRNA half-life: Very abundant mRNAs that are required throughout the life-cycle may be encoded by multicopy genes and have intermediate-to-long half-lives; those encoding ribosomal proteins, with one to two gene copies, are exceptionally stable. Developmentally regulated transcripts with a lower abundance in the bloodstream forms than the procyclic forms had half-lives around the median, whereas those with a higher abundance in the bloodstream forms than the procyclic forms, such as those encoding glycolytic enzymes, had longer half-lives. |
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| Item Description: | Gesehen am 09.08.2022 |
| Physical Description: | Online Resource |
| ISSN: | 1469-9001 |
| DOI: | 10.1261/rna.2837311 |