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| Status |
Public on Sep 26, 2016 |
| Title |
Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination [small RNA-seq] |
| Organism |
Leishmania major |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Base J and H3.V promote RNA Polymerase (RNAP) II termination within polycistronic gene clusters in the kinetoplastid species Trypanosoma brucei. Although base J has been shown to promote RNAP II termination in the related kinetoplastid species Leishmania major and Leishmania tarentolae, the role of H3.V was unclear. The effect of acute J loss on mRNA transcript abundance was also unknown. We find here that H3.V does not promote transcription termination in Leishmania major, but loss of H3.V does reduce J levels. The J loss in H3.V knockout cells is not enough to result in a termination defect, which we show is due to a threshold level of J that is sufficient to promote termination. Loss of J beyond that threshold results in termination defects. Further, the decreased J in H3.V knockout cells allowed greater reduction of J by dimethyloxalylglycine (DMOG), which inhibits J synthesis, compared to wild type cells treated with DMOG, and resulted in stronger defects in RNAP II termination and cell growth. By mRNA-seq we see largely upregulation of genes near the ends of gene clusters following J loss, indicating that J represses genes near termination sites. These findings reveal a conserved role of J in promoting termination prior to the end of polycistronic gene clusters in kinetoplastid parasites and suggest that the essential nature of J is related to its role in repressing genes by promoting termination.
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| Overall design |
The role of base J and H3.V in promoting RNA Polymerase II transcription termination was assessed by small RNA-seq, mRNA-seq, and strand-specific RT-PCR. Wild type cells were compared to H3.V knockout cells and to WT and H3.V knockout cells treated with dimethyloxalylglycine (DMOG) to reduce base J.
This Series represents small RNA-seq samples.
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| Contributor(s) |
Sabatini R, Reynolds DL, Cliffe L, Siegel N, Anderson BA, Beverley SM, Hofmeister BT, Schmitz RJ |
| Citation(s) |
27125778 |
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| Submission date |
Feb 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
David Reynolds |
| E-mail(s) |
dlreynolds6e@gmail.com
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| Organization name |
University of Georgia
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| Department |
Biochemistry and Molecular Biology
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| Lab |
A422
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| Street address |
120 E Green St
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| City |
Athens |
| State/province |
Georgia |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platforms (1) |
| GPL18354 |
Illumina HiSeq 2000 (Leishmania major) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA311271 |
| SRA |
SRP069800 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77713_RAW.tar |
5.5 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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