|
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 |
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) |
GPL16164 |
Illumina HiSeq 2000 (Neurospora crassa) |
|
Samples (3) |
|
This SubSeries is part of SuperSeries: |
GSE61175 |
Neurospora importin alpha compromises H3K9me3 and cytosine methylation levels through inappropriate localization of the heterochromatin machinery |
|
Relations |
BioProject |
PRJNA260402 |
SRA |
SRP046236 |