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Series GSE85127 Query DataSets for GSE85127
Status Public on Mar 30, 2017
Title Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [ChIP-seq_round1]
Organism Schizosaccharomyces pombe
Experiment type Genome binding/occupancy 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 Four pairs of biological replicates: with and without Spt5 C-terminal region, and before and after treatment to deplete Spt5 transcript and protein.
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)
GPL17225 Illumina HiSeq 2500 (Schizosaccharomyces pombe)
Samples (16)
GSM2258061 ChIPseq_Spt5-T0_I_chip
GSM2258062 ChIPseq_Spt5-T4.5_I_chip
GSM2258063 ChIPseq_Spt5-T0_II_chip
This SubSeries is part of SuperSeries:
GSE85182 Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription
BioProject PRJNA336268
SRA SRP080841

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
GSE85127_RAW.tar 263.3 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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