NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE269228 Query DataSets for GSE269228
Status Public on Jun 10, 2024
Title A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in Neurospora crassa [ChIP-Seq]
Organism Neurospora crassa
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genome organization is essential for proper function, including gene expression. In metazoan genome organization, chromatin loops and Topologically Associated Domains (TADs) facilitate local gene clustering, while chromosomes form distinct nuclear territories characterized by compartmentalization of silent heterochromatin at the nuclear periphery and active euchromatin in the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation, where heterochromatic centromeres and telomeres independently cluster at the nuclear membrane, while interspersed heterochromatic loci in Neurospora aggregate across megabases of linear genomic distance for forming TAD-like structures. However, the role of individual heterochromatic loci in normal genome organization and function is unknown. Here, we examined the genome organization of a Neurospora strain harboring a ~41 kilobase facultative (temporarily silent) heterochromatic region deletion, as well as the genome organization of a strain deleted of a ~110 kilobase permanently silent constitutive heterochromatic region. While the facultative heterochromatin deletion had little effect on local chromatin structure, the constitutive heterochromatin deletion altered local TAD-like structures, gene expression, and the predicted 3D genome structure by qualitatively repositioning genes into the nucleus center. Our work elucidates the role of individual heterochromatic regions for genome organization and function.
 
Overall design Chromatin Immunoprecipitation-sequencing (ChIP-seq) of the trimethylation of lysine 9 on histone H3 (H3K9me3) and di- and trimethylation of lysine 27 on histone H3 (H3K27me2/3) from the filamentous fungus Neurospora crassa
 
Contributor(s) Reckard AT, Pandeya A, Voris JM, Gonzalez Cruz CG, Oluwadare O, Klocko AD
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jun 06, 2024
Last update date Jun 10, 2024
Contact name Andrew David Klocko
E-mail(s) aklocko@uccs.edu
Phone 719-255-3255
Organization name University of Colorado Colorado Springs
Department Chemistry and Biochemistry
Lab Klocko
Street address 278 Centennial Hall, 1420 Austin Bluffs Pkwy
City Colorado Springs
State/province Colorado
ZIP/Postal code 80918
Country USA
 
Platforms (1)
GPL26551 Illumina NovaSeq 6000 (Neurospora crassa)
Samples (3)
GSM8309019 NKL2_LGIIK9het25-deletion_H3K9me3_rep1
GSM8309020 NKL2_LGIIK9het25-deletion_H3K9me3_rep2
GSM8309021 WT_N150_H3K27me2-3_rep1
This SubSeries is part of SuperSeries:
GSE269235 A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in Neurospora crassa
Relations
BioProject PRJNA1120777

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE269228_RAW.tar 36.1 Mb (http)(custom) TAR (of BEDGRAPH, BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap