GEO DataSets

(Submitter supplied) Although the advances in genome-wide approaches have elucidated the functions of macrophage-specific distal regulatory elements in transcriptional responses, chromatin structures associated with PU.1 priming and the underlying mechanisms of action of these cis-acting sequences are not characterized. Here, we show that, in macrophages, FACT subunit SPT16 can bind to positioned nucleosomes directly flanking PU.1-bound sites at previously uncharacterized distal regulatory elements located near genes essential for macrophage development and functions. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: BW

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

14 Samples

Download data: BW, WIG

(Submitter supplied) Although the advances in genome-wide approaches have elucidated the functions of macrophage-specific distal regulatory elements in transcriptional responses, chromatin structures associated with PU.1 priming and the underlying mechanisms of action of these cis-acting sequences are not characterized. Here, we show that, in macrophages, FACT subunit SPT16 can bind to positioned nucleosomes directly flanking PU.1-bound sites at previously uncharacterized distal regulatory elements located near genes essential for macrophage development and functions. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

10 Samples

Download data: WIG

(Submitter supplied) Despite its importance during viral or bacterial infections, transcriptional regulation of the interferon-b gene (Ifnb1) in activated macrophages is only partially understood. Here we report that TRIM33 deficiency results in high-sustained expression of Ifnb1 at late stages of toll-like receptor-mediated activation in macrophages but not in fibroblasts. In macrophages, TRIM33 is recruited by PU.1 to a conserved region, Ifnb1 Control Element (ICE), located 15kb upstream of the Ifnb1 transcription start site. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

8 Samples

Download data: BEDGRAPH

(Submitter supplied) To get insight into TRIM33 functions, TRIM33 ChIP-seq was carried out in murine macrophage cell line (RAW) and in bone marrow-derived macrophages (BMDM). The results showed that, in addition to its role in hematopoietic differentiation, TRIM33 may modulate PU.1 transcriptional activity during macrophage development and/or activation.To characterize the role of TRIM33 in macrophages, we bred TRIM33fl/fl mice with Lyz-Cre mice where the Cre recombinase gene is under the regulatory sequences of the Lyz gene that is expressed only in mature myeloid cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

10 Samples

Download data: WIG

(Submitter supplied) FACT consists of two essential subunits Spt16 and Pob3 and is a histone chaperone. Depletion of Spt16 using a an spt16 mutant results in a global alteration of nucleosome positions as well as aberrant transcription. Here we show that the majority of nucleosomal changes at gene body upon Spt16 depletion are independent of gene activity, but correlates with cryptic gene transcription and are suppressed by inhibition of RNA Polymerase II activities. more...

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL13821 GPL9134

28 Samples

Download data: BW

(Submitter supplied) The FACT complex and Spt6 are conserved histone chaperones that are recruited to the open reading frames of transcribed genes. In this study, we provide evidence that FACT interaction with acetylated H3 tail is important for its localization to the coding sequences. Pol II CTD kinase Kin28 additionally stimulates FACT recruitment to a subset of genes. Pol II occupancies in the 5’ ends of transcribed genes are greatly reduced on depleting FACT, whereas reduced occupancies at the 3’ ends were observed upon Spt6 depletion indicating that these factors modulate Pol II progression through distinct regions of transcribed coding sequences. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10930

28 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

141 Samples

Download data: TSV

(Submitter supplied) The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, however our understanding remains limited regarding the molecular determinants of repression. Here we showed that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during mouse alternative macrophage polarization. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TSV

(Submitter supplied) The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, however our understanding remains limited regarding the molecular determinants of repression. Here we showed that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during mouse alternative macrophage polarization. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

53 Samples

Download data: TSV

(Submitter supplied) The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, however our understanding remains limited regarding the molecular determinants of repression. Here we showed that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during mouse alternative macrophage polarization. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: TSV

(Submitter supplied) The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, however our understanding remains limited regarding the molecular determinants of repression. Here we showed that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during mouse alternative macrophage polarization. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TSV

(Submitter supplied) The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, however our understanding remains limited regarding the molecular determinants of repression. Here we showed that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during mouse alternative macrophage polarization. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

64 Samples

Download data: TSV

(Submitter supplied) The molecular basis of signal-dependent transcriptional activation has been extensively studied in macrophage polarization, however our understanding remains limited regarding the molecular determinants of repression. Here we showed that IL-4-activated STAT6 transcription factor is required for the direct transcriptional repression of a large number of genes during mouse alternative macrophage polarization. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TSV

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

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

23 Samples

Download data: BIGWIG

(Submitter supplied) Most mammalian transcription factors and cofactors occupy thousands of genomic sites and modulate the expression of large gene networks to implement their biological functions. In this study, we describe an exception to this paradigm. TRIM33 is identified here as a lineage dependency in B cell neoplasms and is shown to perform this essential function by associating with a single cis element. ChIP-seq analysis of TRIM33 in murine B cell leukemia revealed a preferential association with two lineage-specific enhancers that harbor an exceptional density of motifs recognized by the PU.1 transcription factor. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

19 Samples

Download data: BIGWIG

(Submitter supplied) Most mammalian transcription factors and cofactors occupy thousands of genomic sites and modulate the expression of large gene networks to implement their biological functions. In this study, we describe an exception to this paradigm. TRIM33 is identified here as a lineage dependency in B cell neoplasms and is shown to perform this essential function by associating with a single cis element. ChIP-seq analysis of TRIM33 in murine B cell leukemia revealed a preferential association with two lineage-specific enhancers that harbor an exceptional density of motifs recognized by the PU.1 transcription factor. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT

(Submitter supplied) Most yeast genes have a nucleosome-depleted region (NDR) at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. We have examined the interplay between RSC (a conserved essential SWI/SNF-type complex that determines NDR size) and the ISW1, CHD1 and ISW2 nucleosome spacing enzymes in chromatin organization and transcription, using isogenic strains lacking all combinations of these enzymes. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

6 Samples

Download data: TDF

(Submitter supplied) We addressed the roles of four remodeling machines (ISW1, ISW2, CHD1 and RSC) in specifying the chromatin organization.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13821 GPL19756

32 Samples

Download data: BEDGRAPH

(Submitter supplied) Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter, or subsequently, through regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a key difference between genes that use these distinct regulatory strategies lies in the chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly-regulated genes whose sequences inherently disfavor nucleosome formation within the gene, but favor nucleosomal occlusion of the promoter. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

6 Samples

Download data: CEL, CHP