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| Status |
Public on Jun 10, 2024 |
| Title |
A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in Neurospora crassa [Hi-C] |
| Organism |
Neurospora crassa |
| Experiment type |
Other
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| 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.
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| Overall design |
Chromosome conformation capture coupled with high-throughput sequencing of strains of the filamentous fungus Neurospora crassa deleted of heterochromatic regions, including the N4933 strain deleted of a 47.4 kb facultative heterochromatic region enrichched wiith H3K27me2/3 and the NKL2 (delta LGIK9het25) strain deleted of a 110 kb constitutiive heterochromatic region enriched with H3K9me3.
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| Contributor(s) |
Reckard AT, Pandeya A, Voris JM, Gonzalez Cruz CG, Oluwadare O, Klocko AD |
| Citation(s) |
39229016 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R15 GM140396 |
Genome topology in the filamentous fungus Neurospora crassa: organizing factors and impact on genome function |
UNIVERSITY OF COLORADO COLORADO SPRINGS |
Andrew David Klocko |
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| Submission date |
Jun 06, 2024 |
| Last update date |
Sep 09, 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
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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) |
| GPL20705 |
Illumina HiSeq 2500 (Neurospora crassa) |
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| Samples (8)
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| GSM8309022 |
N4933_delta-K27-region_DpnII-insitu-HiC_rep1 |
| GSM8309023 |
N4933_delta-K27-region_DpnII-insitu-HiC_rep2 |
| GSM8309024 |
NKL2_delta-LGIIK9het25_DpnII-insitu-HiC_rep1 |
| GSM8309025 |
NKL2_delta-LGIIK9het25_DpnII-insitu-HiC_rep2 |
| GSM8309026 |
NKL2_delta-LGIIK9het25_DpnII-insitu-HiC_rep3 |
| GSM8309027 |
NKL2_delta-LGIIK9het25_DpnII-insitu-HiC_rep4 |
| GSM8309028 |
NKL2_delta-LGIIK9het25_MseI-insitu-HiC_rep1 |
| GSM8309029 |
NKL2_delta-LGIIK9het25_MseI-insitu-HiC_rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE269235 |
A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in Neurospora crassa |
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| Relations |
| BioProject |
PRJNA1120776 |
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