NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE104019 Query DataSets for GSE104019
Status Public on Dec 29, 2017
Title Telomere repeats induce domains of H3K27 methylation in Neurospora
Organism Neurospora crassa
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Genome variation profiling by high throughput sequencing
Summary Development in higher organisms requires selective gene silencing, directed in part by di-/tri-methylation of lysine 27 on histone H3 (H3K27me2/3). Knowledge of the cues that control formation of such repressive Polycomb domains is extremely limited. We exploited natural and engineered chromosomal rearrangements in the fungus Neurospora crassa to elucidate the control of H3K27me2/3. Analyses of H3K27me2/3 in strains bearing chromosomal rearrangements revealed both position-dependent and position-independent facultative heterochromatin. We found that proximity to chromosome ends is necessary to maintain, and sufficient to induce, transcriptionally repressive, subtelomeric H3K27me2/3. We ascertained that such telomere-proximal facultative heterochromatin requires native telomere repeats and found that a short array of ectopic telomere repeats, (TTAGGG)17, can induce a large domain (~225 kb) of H3K27me2/3. This provides an example of a cis-acting sequence that directs H3K27 methylation. Our findings provide new insight into the relationship between genome organization and control of heterochromatin formation.
 
Overall design RNA-seq: We analyzed the effects of chromosomal translocations on gene expression changes in Neurospora crassa by poly-A+ mRNA-sequencing performed in duplicate. A wild type strain (N3752) serves as the reference strain (deposited in GSE82222).
ChIP-seq: We analyzed the effects of chromosomal rearrangements and transgenic strains on the distribution of histone H3 lysine 27 methylation (H3K27me2/3) in Neurospora crassa by chromatin immunoprecipitation. Strains were grown, crosslinked, lysed, modified nucleosomes were immunopurified, and associated DNA was sequenced.
Whole-genome-seq: Genomic DNA from chromosomal translocation strains were sequenced and computationally analyzed with LUMPY to identify possible chromosome breakpoints.
 
Contributor(s) Jamieson K, McNaught KJ, Leggett NA, Ormsby T, Honda S, Selker EU
Citation(s) 29297465
NIH grant(s)
Grant ID Grant title Affiliation Name
T32 HD007348 Developmental Biology Training Grant UNIVERSITY OF OREGON Chris Q. Doe
R01 GM093061 Control and Function of Histone H3 Lysine 27 Methylation in Neurospora UNIVERSITY OF OREGON Eric U. SELKER
Submission date Sep 19, 2017
Last update date Jul 25, 2021
Contact name Eric Selker
E-mail(s) selker@uoregon.edu
Organization name University of Oregon
Department Biology
Street address 1370 Franklin Blvd.
City Eugene
State/province Oregon
ZIP/Postal code 97403
Country USA
 
Platforms (2)
GPL20660 Illumina NextSeq 500 (Neurospora crassa)
GPL20705 Illumina HiSeq 2500 (Neurospora crassa)
Samples (34)
GSM2787830 N5100_AR16_FGSC1614_polyA-mRNA
GSM2787831 N5101_ALS159_FGSC2100_polyA-mRNA
GSM2787832 N5102_OY329_FGSC3670_polyA-mRNA
Relations
BioProject PRJNA407972
SRA SRP118137

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
GSE104019_H3K27me2me3_gain_loss_allmutants_DGE.tsv.gz 40.0 Kb (ftp)(http) TSV
GSE104019_RAW.tar 98.5 Mb (http)(custom) TAR (of BEDPE, TDF, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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