GEO DataSets

(Submitter supplied) Chromatin has a highly organized structure with the repeating nucleosome subunits. The position of nucleosomes on the chromatin is dynamically regulated by ATP-dependent chromatin remodeling factors (remodelers), therefore providing specific epigenetic information. However, the in vivo nucleosome distribution pattern in plants and how plant remodelers control the pattern formation are not yet clear. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL17639

2 Samples

Download data: WIG

(Submitter supplied) The Arabidopsis thaliana Imitation Switch (AtISWI) subfamily of ATP-dependent chromatin remodeling factors play essential roles in plant development. Here we show that the DDT domain transcription factor RINGLET (RLT) form a complex with AtISWI. RLT1 physically interacts with CHR11 in yeast cells. Single mutants rlt1-1 and rlt2-1 show no obvious developmental defects, while the rlt1-1 rlt2-1 double mutant phenocopies the AtISWI mutant chr11-1 chr17-1. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) Chromatin remodeling factors of the Imitation Switch (ISWI) family play important roles in epigenetic regulations of gene expression in yeast and animals, whereas their function in plants remains elusive. Here we report characterization of the Arabidopsis ISWI genes CHR11 and CHR17. Double mutant chr11 chr17 displayed a dramatically reduced plant size with early flowering. In addition, epidermis of the double mutant leaves showed cell characteristics seen only in floral organs. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) we identified the forkhead-associated domain 2 (FHA2) as a plant-specific subunit of an ISWI chromatin-remodeling complex in Arabidopsis. By in vivo and in vitro analyses, we demonstrated that FHA2 directly binds to RLT1 and RLT2, two redundant subunits of the ISWI complex in Arabidopsis. A reduced-fertility phenotype was observed in both the fha2 and rlt1/2 mutant plants and the phenotype was ascribed to overgrowth of the pistil during the floral development. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24025

8 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL23157

34 Samples

Download data: BW

(Submitter supplied) We identified three classes of previously uncharacterized plant-specific SWR1 components: MBD9, TRA1a/1b and CHR11/17. We found that CHR11/17 were recruited to the SWR1 complex and facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23157

8 Samples

Download data: BW

(Submitter supplied) We identified three classes of previously uncharacterized plant-specific SWR1 components: MBD9, TRA1a/1b and CHR11/17. We found that CHR11/17 were recruited to the SWR1 complex and facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23157

16 Samples

Download data: BW

(Submitter supplied) We identified three classes of previously uncharacterized plant-specific SWR1 components: MBD9, TRA1a/1b and CHR11/17. We found that CHR11/17 were recruited to the SWR1 complex and facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23157

10 Samples

Download data: TXT, XLS

(Submitter supplied) We propose an interacting barrier mechanism for cooperation between Isw2-related proteins and sequence-specific DNA binding factors.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

49 Samples

Download data: SGR

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL19756

72 Samples

Download data: SGR, TXT

(Submitter supplied) We propose an interacting barrier mechanism for cooperation between Isw2-related proteins and sequence-specific DNA binding factors.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

12 Samples

Download data: TXT

(Submitter supplied) We propose an interacting barrier mechanism for cooperation between Isw2-related proteins and sequence-specific DNA binding factors.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

11 Samples

Download data: TXT

(Submitter supplied) Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with the Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26208

40 Samples

Download data: BW

(Submitter supplied) In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved in plants. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL21785

54 Samples

Download data: BROADPEAK, BW, NARROWPEAK, TXT, WIG

(Submitter supplied) Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

11 Samples

Download data: WIG

(Submitter supplied) Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

7 Samples

Download data: WIG

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

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL13821

18 Samples

Download data: WIG

(Submitter supplied) Comparative study of nuclesome occupancy in Arabidopsis thaliana mutant chr5 and wild type strain.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: BED

(Submitter supplied) We assessed the interplay between DNA sequences and ATP-dependent chromatin remodelers in defining the nucleosomal organization of the eukaryotic genome. We compared the genome-wide distribution and impact on chromatin of NURD, (P)BAP, INO80 and ISWI representing four major families of Drosophila remodelers. Each remodeler has a unique set of genomic targets, and generates distinct chromatin signatures. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

51 Samples

Download data: BAR, BED, CEL, SGR

(Submitter supplied) CAF-1 is a major nucleosome assembly complex, which functions particularly during replication and DNA-repair. Here, we studied how the nucleosome landscape changes in fas2 a mutant of the CAF-1 complex in the model plant Arabidopsis thaliana

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: BED, TSV