GEO DataSets

(Submitter supplied) Pausing of RNA polymerase II (Pol II) during early transcription, mediated by the negative elongation factor (NELF) complex, allows cells to coordinate and appropriately respond to signals by modulating the rate of transcriptional pause release. Promoter proximal enrichment of Pol II occurs at uterine genes relevant to reproductive biology; thus, we hypothesized that pausing might impact endometrial response by coordinating hormonal signals involved in establishing and maintaining pregnancy.We deleted the NELF-B subunit in themouse uterus using PgrCre (NELF-B UtcKO).Resulting females were infertile.Uterine response to the initial decidual stimulus of NELF-B UtcKOwas similar to that of control mice; however, subsequent full decidual response was not observed. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL20775

6 Samples

Download data: CEL, CHP

(Submitter supplied) Ovarian estrogen (E2) and progesterone (P4) are indispensable for embryo-implantation and endometrial stromal decidualization; however, the molecular mechanisms that underpin these reproductive processes are unclear. Steroid receptor coregulator-2 (SRC-2) belongs to the multifunctional SRC/p160 family which also includes SRC-1 and SRC-3. Sharing strong sequence homology, all three SRCs exert diverse regulatory effects by modulating the transcriptional potency of nuclear receptor family members, including the estrogen and progesterone receptor (ER and PR respectively). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4866

Platform:

GPL1261

12 Samples

Download data: CEL

Analysis of uteri from steroid receptor coregulator-2 (SRC-2) mutants that were ovariectomized at 6 weeks and treated with progesterone (P4) 2 weeks later. SRC-2 is a member of the p160/SRC family of coregulators. Results provide mechanistic insight into SRC-2's role in endometrial decidualization.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 agent, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE31406

12 Samples

Download data: CEL

(Submitter supplied) Our findings establish a key role for the coregulator, Repressor of Estrogen receptor Activity (REA), in controlling the timing and magnitude of decidualization in human endometrial stromal cells in vitro and in the mouse uterus in vivo, and suggest that REA functions to synchronize uterine differentiation with concurrent embryo development, which is essential for optimal implantation and fertility. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

8 Samples

Download data: CEL

(Submitter supplied) We report the transcriptomic profile of primary human endometrial stromal cells subjected to 48-hour transfection with control non-targeting siRNA or siRNA targeting WNK1 followed by 3-day in vitro decidualization treatment.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL9250 GPL6885

6 Samples

Download data: BED

(Submitter supplied) Many mammalian genes are occupied by paused RNA polymerase II (pol II) at promoter-proximal regions on both sides of transcription start sites (TSSs). However, the consequences of pol II pausing on gene expression and cell biology are not fully understood. Here we report that genetic ablation of the b subunit of mouse negative elongation factor (Nelf-b), a key pol II-pausing factor, results in slower progression at multiple cell cycle stages and increased apoptosis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

4 Samples

Download data: TXT

(Submitter supplied) Many mammalian genes are occupied by paused RNA polymerase II (pol II) at promoter-proximal regions on both sides of transcription start sites (TSSs). However, the consequences of pol II pausing on gene expression and cell biology are not fully understood. Here we report that genetic ablation of the b subunit of mouse negative elongation factor (Nelf-b), a key pol II-pausing factor, results in slower progression at multiple cell cycle stages and increased apoptosis. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: BED

(Submitter supplied) RNA-sequencing of mRNA isolated from in vitro decidualizaing human endometrial stromal cells with or without siRNA-mediated knockdown of PLZF

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) RNA polymerase II (Pol II) is generally paused at promoter-proximal regions in most metazoans, and based on in vitro studies, this function has been attributed to the negative elongation factor (NELF). Here, we show that upon rapid depletion of NELF, Pol II fails to be released into gene bodies, stopping instead around the +1 nucleosomal dyad-associated region. The transition to the 2nd pause region is independent of positive transcription elongation factor P-TEFb. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL18573

69 Samples

Download data: BW

(Submitter supplied) The current work describes molecular mechanism used by the Negative elongation complex (NELF) to control the Pol II pause at genes whose transcription is induced by 20-hydroxyecdysone (20E). According to our data NELF complex is recruited to the promoters and enhancers of 20E-dependent genes. Its presence at the regulatory sites of 20E-dependent genes correlates with the described interaction of its NELF-A subunit with EcR receptor. more...

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL25244

53 Samples

Download data: BIGWIG, TXT

(Submitter supplied) To test whether Brd4 and SEC co-regulate the release of promoter-proximally paused Pol II, we performed Pol II ChIP-Seq to analyze the effect of depletion of Brd4 or SEC on HMBA-induced pause release in HCT116 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: BED

(Submitter supplied) Negative elongation factor (NELF) is known to enforce promoter-proximal pausing of RNA polymerase II (Pol II), a pervasive phenomenon observed across multicellular genomes. However, the physiological impact of NELF on tissue homeostasis remains unclear. Here we show for the first time that whole-body conditional deletion of the B subunit of NELF (NELF-B) in adult mice results in cardiomyopathy and impaired response to cardiac stress. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5302

Platform:

GPL6885

6 Samples

Download data: TXT

Analysis of heart left ventricles from mutants lacking the B subunit of negative elongation factor (NELF). NELF is a regulator of RNA polymerase II pausing. Results provide insight into the role of NELF in myocardial function.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL6885

Series:

GSE54372

6 Samples

Download data

(Submitter supplied) Biochemical studies have established that the four-subunit negative elongation factor (NELF) complex mediates RNA polymerase II (Pol II) pausing at promoter proximal regions. Genetic ablation of individual NELF subunits destabilizes the entire NELF complex and causes lethality of cultured cells, leading to the prevailing concept that NELF-mediated Pol II pausing is essential for cell survival. Using separation-of-function mutations, we show here that NELFB’s effects on cell proliferation can be uncoupled from its function in Pol II pausing. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL21493

47 Samples

Download data: BW

(Submitter supplied) Biochemical studies have established that the four-subunit negative elongation factor (NELF) complex mediates RNA polymerase II (Pol II) pausing at promoter proximal regions. Genetic ablation of individual NELF subunits destabilizes the entire NELF complex and causes lethality of cultured cells, leading to the prevailing concept that NELF-mediated Pol II pausing is essential for cell survival. Using separation-of-function mutations, we show here that NELFB’s effects on cell proliferation can be uncoupled from its function in Pol II pausing. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

35 Samples

Download data: TXT

(Submitter supplied) The human Negative Elongation Factor (NELF) is a four-subunit protein complex that inhibits the movement of RNA polymerase II (RNAPII) at an early elongation stage in vitro. NELF-mediated stalling of RNAPII also attenuates transcription of a number of inducible genes in human cells. To obtain a genome-wide understanding of human NELF-mediated transcriptional regulation in vivo, we carried out an exon-array study in T47D breast cancer cells with transient siRNA knockdown of individual NELF subunits. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5175 GPL5188

30 Samples

Download data: CEL, CHP

(Submitter supplied) Cdk9 is an essential transcriptional kinase that is conserved across distant eukaryotes, but we previously found that acute inhibition of Cdk9 causes different transcriptional phenotypes in NELF-containing higher eukaryotes (like mammals and Drosophila) vs. the NELF-lacking fission yeast S. pombe. NELF is known to participate in promoter-proximal pausing of RNA Polymerase II, and using NELF-depleted Drosophila cells,  we find that this NELF-mediated pause is necessary to prevent gene body entry by Pol II in the absence of Cdk9. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL22106 GPL19132

30 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) The ERK pathway induces cell proliferation in response to growth factor stimulation. Although ERK controls various transcription factors in the nucleus, gene regulation mechanisms underlying the rapid IEG inductions were not fully elucidated. Here we report that ERK phosphorylates an unique novel substrate. We found that ERK facilitates rapid transcription of IEGs through the phosphorylation of the substrate.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

12 Samples

Download data: XLS, XLSX

(Submitter supplied) Transforming growth factor β (TGFβ) signaling regulates multifaceted reproductive processes via its transmembrane receptor complex-associated machinery. It has been shown that the type 1 receptor of TGFβ (TGFBR1) is indispensable for female reproductive tract development, pregnancy success, and fertility. However, the role of TGFβ signaling in decidual development and function remains poorly defined. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: XLSX