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Series GSE85124 Query DataSets for GSE85124
Status Public on Mar 30, 2017
Title Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [NET-seq]
Organism Schizosaccharomyces pombe
Experiment type Other
Expression profiling by high throughput sequencing
Summary Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. However, the genome-wide requirement for Spt5 in transcription has not been extensively studied. To address this issue, we have comprehensively analyzed the consequences of Spt5 depletion on transcription by RNAPII in Schizosaccharomyces pombe using four genome-wide approaches: ChIP-seq, NET-seq, 4tU-seq, and RNA-seq. Our results demonstrate that, in the absence of Spt5, RNAPII accumulates at a high level over the first ~500 bp of transcription units, suggesting that Spt5 is globally required to elongate past a barrier to transcription. This possibility is strongly supported by results showing that Spt5 is required for a normal level of RNA synthesis. In addition to these effects on sense-strand transcription, Spt5 depletion results in widespread convergent antisense transcription that initiates at approximately the same position as the sense-strand barrier. While the role of these antisense transcripts is unknown, the two that were tested control the distribution of RNAPII. Our results also show that Spt5 represses divergent antisense transcription, explaining why it has not been previously observed in S. pombe. Taken together, our results reveal a global and critical role for Spt5 in multiple classes of transcription by RNAPII.
Overall design Two pairs of biological replicates before and after treatment to deplete Spt5 transcript and protein. T0_I was taken from a separate experiment (1) because the other T0 replicate in experiment 2 showed high rate of PCR duplication.
Contributor(s) Shetty A, Kallgren SP, Alver BH, Park PJ, Winston F
Citation(s) 28366642
Submission date Aug 03, 2016
Last update date May 15, 2019
Contact name Peter J Park
Phone 617-432-7373
Organization name Harvard Medical School
Department Center for Biomedical Informatics
Street address 10 Shattuck St
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL13988 Illumina HiSeq 2000 (Schizosaccharomyces pombe)
Samples (4)
GSM2258030 NETseq_Spt5_T0_I
GSM2258031 NETseq_Spt5_T0_II
GSM2258032 NETseq_Spt5_T4.5_I
This SubSeries is part of SuperSeries:
GSE85182 Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription
BioProject PRJNA336265
SRA SRP080842

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE85124_RAW.tar 20.3 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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