GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE61174 Query DataSets for GSE61174
Status Public on Mar 22, 2015
Title Bisulfite-seq from Neurospora crassa a wild type (WT) strain grown in minimum medium, a dim-3 strain grown in minimum medium, and a dim-3 strain grown with supplemented histidine
Organism Neurospora crassa
Experiment type Methylation profiling by high throughput sequencing
Summary 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. NUP-6(dim-3) compromises the heterochromatic localization of several components of the DCDC, a histone H3K9 methyltransferase complex, which in turn reduces the level of Heterochromatin Protein-1 (HP1) found at heterochromatin and compromises the direct interaction between HP1 and the DNA methyltransferase dim-2. To determine whether the reduced level of cytosine methylation, as assayed by Southern blotting heterochromatic regions following digestion of genomic DNA with methylation-sensitive restriction endonucleases, is globally reduced at the A:T rich, repetitive DNA comprising heterochromatin, we performed Bisulfite-seq on a dim-3 strain (grown either in minimal medium or medium supplemented with histidine) and compared that to a wild type strain (grown in minimum medium; histidine does not reduce the levels of cytosine methylation in a wild type strain, as assayed by Southern blotting).
Overall design Examination of cytosine methylation, as determined by bisulfite treatment, of two strains (a wild type strain and a dim-3 strain; the dim-3 strain was grown in two different conditions)
Contributor(s) Klocko AD, Rountree MR, Selker EU
Citation(s) 25793375
NIH grant(s)
Grant ID Grant title Affiliation Name
F32 GM097821 Genetic analysis of DNA methylation in Neurospora crassa UNIVERSITY OF OREGON KLOCKO
R01 GM035690 Genetic Aspects of DNA Methylation UNIVERSITY OF OREGON SELKER
R37 GM035690 Genetic Aspects of DNA Methylation UNIVERSITY OF OREGON SELKER
Submission date Sep 05, 2014
Last update date Feb 11, 2021
Contact name Andrew David Klocko
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)
GPL16164 Illumina HiSeq 2000 (Neurospora crassa)
Samples (3)
GSM1498893 WT_Ncrassa_BSseq
GSM1498894 dim-3_min_Ncrassa_BSseq
GSM1498895 dim-3_+his_Ncrassa_BSseq
This SubSeries is part of SuperSeries:
GSE61175 Neurospora importin alpha compromises H3K9me3 and cytosine methylation levels through inappropriate localization of the heterochromatin machinery
BioProject PRJNA260402
SRA SRP046236

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
GSE61174_RAW.tar 1.5 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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