GEO DataSets

(Submitter supplied) Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes: in the fungus Neurospora crassa, chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures that are anchored by heterochromatic region aggregates. However, insufficient information exists on how histone post-translational modifications, including acetylation, impact genome organization. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26551

19 Samples

Download data: BEDGRAPH, BIGWIG, BW

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

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL23150 GPL26551

31 Samples

Download data: BEDGRAPH, BIGWIG, BW, H5

(Submitter supplied) Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes: in the fungus Neurospora crassa, chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures that are anchored by heterochromatic region aggregates. However, insufficient information exists on how histone post-translational modifications, including acetylation, impact genome organization. more...

Organism:

Neurospora crassa

Type:

Other

Platforms:

GPL23150 GPL26551

12 Samples

Download data: H5

(Submitter supplied) Whole-Genome Bisulfite Sequencing of HCHC mutants To extend our understanding of the role of the HCHC complex in Neurospora, we carried out whole-genome bisulfite sequencing (WGBS) of cdp-2, chap, and hda-1 mutants.  Consistent with prior analyses, the WGBS revealed both hypomethylated and hypermethylated regions in the three HCHC mutants while the ; sequences with a lower Combined RIP Index (CRI) tend to show reduced methylation in the mutants, while sequences with higher CRI scores show increased methylation. more...

Organism:

Neurospora crassa

Type:

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

Platform:

GPL16164

7 Samples

Download data: IGV, TDF

(Submitter supplied) Purpose: The goal of this study is to characterize the domain(s) of H3K9me3 induced by artifical localization of heterochromatin factors in wild-type and mutant backgrounds.

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23150

6 Samples

Download data: TDF, TXT

(Submitter supplied) Eukaryotic genomes are organized into chromatin domains with distinct three-dimensional arrangements resulting from nucleic acid and protein factor interactions within the physical constraints of the nucleus. It is of obvious interest to determine interactions between various chromosomal regions defined by these nuclear constraints, and to identify important factors that limit the interactions. We used chromosome conformation capture (3C) followed by high-throughput sequencing (HiC) to improve our understanding of Neurospora crassa genome organization and to examine if known components of heterochromatin machinery influence nuclear organization. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL20705

5 Samples

Download data: FASTA, GTF, TDF, TXT

(Submitter supplied) Both RNAi-dependent and -independent mechanisms have been implicated in the establishment of heterochromatin domains, which may be stabilized by feedback loops involving chromatin proteins and modifications of histones and DNA. Neurospora crassa sports features of heterochromatin found in higher eukaryotes, namely cytosine methylation (5mC), methylation of histone H3 lysine9 (H3K9me) and HETEROCHROMATIN PROTEIN-1 (HP1), and provides a model to investigate heterochromatin establishment and maintenance. more...

Organism:

Neurospora crassa

Type:

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

Platform:

GPL7253

13 Samples

Download data: GPR

(Submitter supplied) Aberrant DNA methylation is often associated with cancers and DNA-demethylating agents such as 5-azacytidine (5-azaC) are often used for anti-tumor therapy. Although it is clinically effective at inhibiting DNA methylation, the mechanistic effect that 5-azaC elicits on eukaryotic cells is controversial. It has been proposed that incorporation of 5-azaC into DNA during replication irreversibly tethers cytosine methyltransferases (MTases) to DNA. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL20660 GPL16164

19 Samples

Download data: FASTA, IGV, TDF, TXT, VCF, WIG

(Submitter supplied) For a eukaryotic genome to properly function, its chromatin must be precisely organized, as genome topology impacts transcriptional regulation, cell division, DNA replication, and DNA repair, among other essential processes. Disruption of human genome topology can lead to disease states, such as cancer. The advent of chromosome conformation capture with high-throughput sequencing (Hi-C) technologies to assess genome organization has revolutionized our understanding of the arrangement of chromosomes within the nuclear genome. more...

Organism:

Neurospora crassa

Type:

Other

Platforms:

GPL26551 GPL23150

10 Samples

Download data: FASTA, GTF, H5

(Submitter supplied) Both H3K9me3 and DNA methylation are subject to spreading mechanisms to effectively cover incipient chromatin across heterochromatin domains. Boundary elements and associated limiting factors are necessary to prevent heterochromatin from spreading into neighboring, gene-rich heterochromatin. LSD1 was identified to be one such factor, given previous studies in other models and high conservation throughout eukaryotes. more...

Organism:

Neurospora crassa

Type:

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

Platforms:

GPL23150 GPL20660 GPL16164

16 Samples

Download data: BED, BIGWIG, IGV, TDF, TXT

(Submitter supplied) Facultative heterochromatin in the filamentous fungus Neurospora crassa is identified by the repressive histone mark H3K27me3 and is primarily subtelomeric, while constitutive heterochromatin, marked by the DIM-5-catalzyed H3K9me3, is found at centromeres, telomeres, and smaller dispersed regions. In strains lacking constitutive heterochromatin (e.g., Δdim-5), H3K27me2/3 relocalizes to the regions formerly marked by H3K9me3. more...

Organism:

Neurospora crassa

Type:

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

Platforms:

GPL20705 GPL20660

16 Samples

Download data: BCF, FASTA, GTF, TDF, TXT, XLSX

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

Organism:

Neurospora crassa

Type:

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

Platform:

GPL16164

5 Samples

Download data: TDF, WIG

(Submitter supplied) We report the placement of cytosine methylation from the filamentous fungus Neurospora crassa in wild type and dim-3 strains by bisulfite-sequencing. Compared to a wild type strain, the dim-3 strain has a global reduction in cytosine methylation, and this reduction in cytosine methylation is exacerbated by the supplementation of histidine to the growth medium. This global reduction in cytosine methylation results from a causative mutation in importin alpha (NUP-6), a component of the nuclear transport machinery, which severely reduces the level of the heterochromatic mark H3K9me3. more...

Organism:

Neurospora crassa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16164

3 Samples

Download data: WIG

(Submitter supplied) We report the placement of the H3K9me3 heterochromatin mark from the filamentous fungus Neurospora crassa in wild type and dim-3 strains. The dim-3 strain has a global reduction in H3K9me3, which results from a causative mutation in importin alpha (NUP-6), a component of the nuclear transport machinery. NUP-6(dim-3) compromises the heterochromatic localization of several components of the DCDC, a histone H3K9 methyltransferase complex, from their sub-nuclear chromatin targets despite appropriate nuclear transport. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16164

2 Samples

Download data: TDF

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

Organism:

Neurospora crassa

Type:

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

Platform:

GPL20705

32 Samples

Download data

(Submitter supplied) Sensing and responding to light provides organisms an adaptive advantage, in part by altering gene expression. The complement of light-activated genes in model organisms is largely known, and some of the mechanisms by which proteins modulate the light response are likewise well defined. However, how light alters post translation modifications to chromatin and how changes in chromatin facilitates and/or inhibit changes in gene expression has not been examined in depth. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20705

12 Samples

Download data: FPKM_TRACKING, GTF

(Submitter supplied) Sensing and responding to light provides organisms an adaptive advantage, in part by altering gene expression. The complement of light-activated genes in model organisms is largely known, and some of the mechanisms by which proteins modulate the light response are likewise well defined. However, how light alters post translation modifications to chromatin and how changes in chromatin facilitates and/or inhibit changes in gene expression has not been examined in depth. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20705

20 Samples

Download data: BED

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

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL22765

8 Samples

Download data: BW, TXT

(Submitter supplied) Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explored mechanisms controlling genome compartment organization in C. elegans and investigated roles for compartments in regulating gene expression. The distal arms of C. elegans chromosomes, which are enriched for heterochromatic histone modifications including H3K9me, interact with each other both in cis and in trans, while interacting less frequently with central regions of chromosomes, leading to genome compartmentalization. more...

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL22765

2 Samples

Download data: TXT

(Submitter supplied) Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explored mechanisms controlling genome compartment organization in C. elegans and investigated roles for compartments in regulating gene expression. The distal arms of C. elegans chromosomes, which are enriched for heterochromatic histone modifications including H3K9me, interact with each other both in cis and in trans, while interacting less frequently with central regions of chromosomes, leading to genome compartmentalization. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22765

6 Samples

Download data: BW