GEO DataSets

(Submitter supplied) DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer. Here we analyze genome-wide binding and function of the C. elegans DRM subunit LIN-54. We demonstrate that LIN-54 DNA-binding activity is required for the DRM complex to efficiently bind and regulate target genes containing adjacent putative E2F/DP and LIN-54 binding sites. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL7484 GPL7483 GPL7482

6 Samples

Download data: TXT

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

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

4 related Platforms

18 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer. Here we perform microarray expression profiling analysis of lin-54, a DNA-binding member of the DRM complex. To identify genes regulated by LIN-54 in soma and germline, we analyzed wild-type and lin-54 mutant C. elegans embryos and isolated germlines. We chose embryos because they consist primarily of somatic cells, at a developmental stage with both active cell divisions and dynamic developmental gene expression programs. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

12 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Here we uncover antagonistic regulation of transcript levels in the germline of Caenorhabditis elegans hermaphrodites. The histone methyltransferase MES-4 marks genes expressed in the germline with methylated Lys36 on histone H3 (H3K36me) and promotes their transcription; MES-4 also represses genes normally expressed in somatic cells and genes on the X chromosomes. The DRM complex, which includes E2F/DP and Retinoblastoma homologs, affects germline gene expression and prevents excessive repression of X-chromosome genes. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

12 Samples

Download data: CEL

(Submitter supplied) Microarray-based expression profiling of dissected gonads from efl-1, dpl-1 and lin-35 mutants reveals that EFL-1 and DPL-1 promote expression of an extensively overlapping set of target genes, consistent with the expectation that these two proteins function as a heterodimer. Regulatory regions upstream of many of these target genes have a canonical E2F binding site, suggesting that their regulation by EFL-1/DPL-1 is direct. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platforms:

GPL3859 GPL3860

10 Samples

Download data

(Submitter supplied) The highly conserved DREAM transcriptional repressor complex contains an RB-like pocket protein, an E2F-DP transcription factor heterodimer, and the 5-subunit MuvB complex. Using CRISPR/Cas9 targeted mutagenesis, we disrupted the interaction between the sole Caenorhabditis elegans pocket protein LIN-35 and the MuvB subunit LIN-52. A triple alanine substitution of LIN-52's LxCxE motif (3A) severed LIN-35-MuvB association and caused classical DREAM mutant phenotypes, including synthetic multiple vulvae, high-temperature arrest, and ectopic expression of germline genes in the soma. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25147

8 Samples

Download data: TXT

(Submitter supplied) The Retinoblastoma-like pocket proteins p130 and p107 act as gatekeepers of the cell cycle through their activity within the DREAM (Dp/Rb-like/E2F/MuvB) transcriptional repressor complex. The goal of this study was to address how the pocket protein contributes to DREAM complex assembly and function on chromatin by utilizing a protein null mutant of the only C. elegans pocket protein LIN-35. We performed ChIP-seq of C. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL22765 GPL13657 GPL9269

46 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) The Rb/E2F tumor suppressor regulates gene expression to control the onset and timing of differentiation in many different cell types during development. This critical function makes Rb/E2F a frequent target for inactivation in tumors of diverse tissue origin. However, the mechanisms by which Rb/E2F governs tissue-specific gene regulation in vivo are poorly understood. We have determined the genome-wide binding profiles for components of the C. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13776

48 Samples

Download data: BEDGRAPH, GFF3

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

Organism:

Caenorhabditis elegans

Type:

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

4 related Platforms

91 Samples

Download data: BEDGRAPH, BROADPEAK, GFF, GPR, NARROWPEAK, PAIR, WIG

(Submitter supplied) synMuv B proteins, including LIN-15B, are necessary to repress the expression of germline-promoting genes in the soma during embryonic and early larval development in C. elegans. The goal of this research was to determine if changes to histone modifications could underlie the misexpression of germline genes in these mutants. We performed ChIP-seq on four histone modifications in wild type and three synMuv B mutants at two temperatures to assess these changes.

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL22765 GPL13657

78 Samples

Download data: BEDGRAPH, BROADPEAK, NARROWPEAK

(Submitter supplied) Here we exploit the essential process of X-chromosome dosage compensation to elucidate basic mechanisms that control the assembly, genome-wide binding, and function of gene regulatory complexes that act over large chromosomal territories. We demonstrate that a subunit of C. elegans MLL/COMPASS, a gene-activation complex, acts within the dosage compensation complex (DCC), a condensin complex, to target the DCC to both X chromosomes of hermaphrodites and thereby reduce chromosome-wide gene expression. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8134

3 Samples

Download data: GFF, PAIR

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

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL200 GPL8134

53 Samples

Download data: CEL, CHP, GFF, PAIR

(Submitter supplied) Here we exploit the essential process of X-chromosome dosage compensation to elucidate basic mechanisms that control the assembly, genome-wide binding, and function of gene regulatory complexes that act over large chromosomal territories. We demonstrate that a subunit of C. elegans MLL/COMPASS, a gene-activation complex, acts within the dosage compensation complex (DCC), a condensin complex, to target the DCC to both X chromosomes of hermaphrodites and thereby reduce chromosome-wide gene expression. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8134

44 Samples

Download data: GFF, PAIR

(Submitter supplied) Here we exploit the essential process of X‐chromosome dosage compensation to elucidate basic mechanisms that control the assembly, genome‐wide binding, and function of gene regulatory complexes that act over large chromosomal territories. We demonstrate that a subunit of C. elegans MLL/COMPASS, a gene-activation complex, acts within the dosage compensation complex (DCC), a condensin complex, to target the DCC to both X chromosomes of hermaphrodites and thereby reduce chromosome-wide gene expression. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

6 Samples

Download data: CEL, CHP

(Submitter supplied) A temporal gradient of the novel nuclear protein LIN-14 specifies the timing and sequence of stage-specific developmental events in Caenorhabditis elegans. The profound effects of lin-14 mutations on worm development suggest that LIN-14 directly or indirectly regulates stage-specific gene expression. We show that LIN-14 can associate with chromatin in vivo and has in vitro DNA binding activity. A bacterially expressed C-terminal domain of LIN-14 was used to select DNA sequences that contain a putative consensus binding site from a pool of randomized double-stranded oligonucleotides. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platforms:

GPL14 GPL2646

6 Samples

Download data

(Submitter supplied) Maternally synthesized products play critical roles in development of offspring. A premier example is the C. elegans H3K36 methyltransferase MES-4, which is essential for germline survival and development in offspring. How maternal MES-4 protects the germline is not well understood, but its role in H3K36 methylation hinted that it may regulate gene expression in Primordial Germ Cells (PGCs). We tested this hypothesis by profiling transcripts from nascent germlines (PGCs and their descendants) dissected from wild-type and mes-4 mutant (lacking maternal and zygotic MES-4) larvae. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18245 GPL26672

132 Samples

Download data: TXT

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

Organism:

Caenorhabditis elegans

Type:

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

Platform:

GPL18730

81 Samples

Download data: BW

(Submitter supplied) The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18730

31 Samples

Download data: BW

(Submitter supplied) The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18730

50 Samples

Download data: BW

(Submitter supplied) modENCODE_submission_2623 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9309

4 Samples

Download data: BEDGRAPH, GFF3