GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

5 related Platforms

70 Samples

Download data: CEL, TXT

(Submitter supplied) Topoisomerases are necessary for the expression of neurodevelopmental genes, and are mutated in some patients with autism spectrum disorder (ASD). We have studied the effects of inhibitors of Topoisomerase 1 (Top1) and Topoisomerase 2 (Top2) enzymes on mouse cortical neurons. We find that topoisomerases selectively inhibit long genes (>100kb), with little effect on all other gene expression. Using ChIPseq against RNA Polymerase II (Pol2) we show that the Top1 inhibitor topotecan blocks transcriptional elongation of long genes specifically. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL1261 GPL17400 GPL11533

56 Samples

Download data: CEL

(Submitter supplied) Topoisomerases are necessary for the expression of neurodevelopmental genes, and are mutated in some patients with autism spectrum disorder (ASD). We have studied the effects of inhibitors of Topoisomerase 1 (Top1) and Topoisomerase 2 (Top2) enzymes on mouse cortical neurons. We find that topoisomerases selectively inhibit long genes (>100kb), with little effect on all other gene expression. Using ChIPseq against RNA Polymerase II (Pol2) we show that the Top1 inhibitor topotecan blocks transcriptional elongation of long genes specifically. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

14 Samples

Download data: TXT

(Submitter supplied) Topoisomerase 1 (TOP1) inhibitors, including camptothecin and topotecan, covalently trap TOP1 on DNA, creating cleavage complexes (cc’s) that must be resolved before gene transcription and DNA replication can proceed. We previously found that topotecan reduces the expression of long (>100 kb) genes and unsilences the paternal allele of Ube3a in neurons. Here, we sought to evaluate overlap between TOP1cc-dependent and -independent gene regulation in neurons. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) DNA topoisomerases are known to promote transcription in prokaryotes by removing excessive DNA supercoils produced during elongation. However, it is unclear how topoisomerases in eukaryotes are recruited and function in the transcription pathway in the context of nucleosomes. To address this problem we present high-resolution genome wide maps of one of the major eukaryotic topoisomerases, Topoisomerase II (Top2) and nucleosomes in the budding yeast, Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4130 GPL7250

15 Samples

Download data: BAR, CEL, TSV, TXT

(Submitter supplied) We report a mechanism through which the transcription machinery directly controls topoisomerase 1 (TOP1) activity to adjust DNA topology throughout the transcription cycle. By comparing TOP1 occupancy using ChIP-Seq, versus TOP1 activity using TOP1-Seq, a method reported here to map catalytically engaged TOP1, TOP1 bound at promoters was discovered to become fully active only after pause-release. This transition coupled the phosphorylation of the carboxyl-terminal-domain (CTD) of RNA polymerase II (RNAPII) with stimulation of TOP1 above its basal rate, enhancing its processivity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL9115 GPL9520

27 Samples

Download data: TXT, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL21697

37 Samples

Download data: BW

(Submitter supplied) High-intensity transcription and replication supercoil DNA to levels that can impede or halt these processes. As a potent transcription amplifier and replication accelerator, the proto-oncogene MYC must somehow manage these high levels of torsional stress. By comparing gene expression with the recruitment of topoisomerases and MYC to promoters, we surmised a direct association of MYC with Topoisomerases 1 (TOP1) and 2A (TOP2A) that was confirmed in vitro and in vivo. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

13 Samples

Download data: BW

(Submitter supplied) High-intensity transcription and replication supercoil DNA to levels that can impede or halt these processes. As a potent transcription amplifier and replication accelerator, the proto-oncogene MYC must somehow manage these high levels of torsional stress. By comparing gene expression with the recruitment of topoisomerases and MYC to promoters, we surmised a direct association of MYC with Topoisomerases 1 (TOP1) and 2A (TOP2A) that was confirmed in vitro and in vivo. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

4 Samples

Download data: BW

(Submitter supplied) High-intensity transcription and replication supercoil DNA to levels that can impede or halt these processes. As a potent transcription amplifier and replication accelerator, the proto-oncogene MYC must somehow manage these high levels of torsional stress. By comparing gene expression with the recruitment of topoisomerases and MYC to promoters, we surmised a direct association of MYC with Topoisomerases 1 (TOP1) and 2A (TOP2A) that was confirmed in vitro and in vivo. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

20 Samples

Download data: BW, XLSX

(Submitter supplied) The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a “cleavable complex”. To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment affected transcription initiation, elongation, termination, splicing and enhancer activity. Following removal of camptothecin, transcription spread as a wave from the 5’-end of genes with no recovery of transcription apparent from RNA polymerases stalled in the body of genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: TXT

(Submitter supplied) Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Δtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9281

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL9282 GPL9281

21 Samples

Download data: TXT

(Submitter supplied) Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Δtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9282

6 Samples

Download data: TXT

(Submitter supplied) Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Δtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9281

9 Samples

Download data: TXT

(Submitter supplied) Genomic Run-on analysis of topoisomerase mutants (top1-delta/top2ts or top2ts) has been conducted at reference temperature for wt strain and at non-permissive temperature for wt and mutant strains. Keywords: Genomic Run On

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7871

13 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platform:

GPL21697

60 Samples

Download data: BW

(Submitter supplied) Using SLAM-seq to capture de novo synthesized polyadenylated RNAs, we quantitated changes in nascent RNA expression, as well as in total RNA expression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21697

12 Samples

Download data: CSV

(Submitter supplied) By following chromatin occupancy of RNAPII and TOP1 using ChIP-seq throughout mitosis, we found that TOP1 is required for RNAPII translocation along genes. The stimulation of TOP1 activity through its interaction with RNAPII during elongation, allowed RNAPII clearance from genes in prometaphase and enabled proper chromosomal segregation. Interference with the TOP1-RNAPII interaction or acute depletion of TOP1 at the onset of mitosis impaired RNAPII spiking at promoters, which is necessary for the first pioneering round of transcription during mitotic exit, and triggered defects in the transcriptional program of the post-mitotic cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

48 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data