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| 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
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| 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).
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| 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)
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| 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 |
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| Submission date |
Sep 05, 2014 |
| Last update date |
Feb 11, 2021 |
| Contact name |
Andrew David Klocko |
| E-mail(s) |
aklocko@uccs.edu
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| Phone |
719-255-3255
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| Organization name |
University of Colorado Colorado Springs
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| Department |
Chemistry and Biochemistry
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| Lab |
Klocko
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| Street address |
278 Centennial Hall, 1420 Austin Bluffs Pkwy
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| City |
Colorado Springs |
| State/province |
Colorado |
| ZIP/Postal code |
80918 |
| Country |
USA |
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| Platforms (1) |
| GPL16164 |
Illumina HiSeq 2000 (Neurospora crassa) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE61175 |
Neurospora importin alpha compromises H3K9me3 and cytosine methylation levels through inappropriate localization of the heterochromatin machinery |
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| Relations |
| BioProject |
PRJNA260402 |
| SRA |
SRP046236 |
