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| Status |
Public on Jul 09, 2021 |
| Title |
Genetic Adaptation of C. elegans to Environment Changes II: Multigenerational Analysis of Genome-wide Chromatin Remodeling |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Chemical modifications to the tails of histone proteins act as gene regulators that play a pivotal role in adaptive responses to environmental stress. Determining the short and long term kinetics of histone marks is essential for understanding their functions in adaptation. We used Caenorhabditis elegans as a model organism to study the histone modification kinetics in response to environmental stress, taking advantage of their ability to live in both terrestrial and aquatic environments. We investigated the multigenerational genome-wide dynamics of five histone marks (H3K4me3, H3K27me3, H4K20me1, H3K36me1, and H3K9me3) by maintaining P0 animals on terrestrial (agar plates), F1 in aquatic cultures, and F2 back on terrestrial environments. We determined the distributions of histone marks in the gene promoter regions and found that H4K20me1, H3K36me1, and H3K9me3 showed up to eleven-fold differences in density, whereas H3K4me3 and H3K27me3 remained highly constant during adaptation from terrestrial to aquatic environments. Furthermore, we predicted that up to five combinations of histone marks can co-occupy single gene promoters and confirmed the colocalization of these histone marks by structured illumination microscopy. The co-occupancy increases with environment changes and different co-occupancy patterns contribute to variances in gene expressions and thereby presents a supporting evidence for the histone code hypothesis.
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| Overall design |
In order to elicit an adaptive response, the C. elegans P0 generation was grown on bacteria-seeded agar plates (OP50 NGM), the F1 generation was transferred to liquid, and the F2 generation reverted to agar. In addition to the changes in the physical environment, i.e., agar to liquid, we examined the effect of the dietary changes in the liquid cultures by using two different growth media: the commonly used bacterial S-Medium and more exotic axenic CeHR medium. For each generation, ChIP-seq was used to determine the distributions of the five histone modifications across the genome. The ChIP-seq libraries were generated with two replicates. N2 strain was used for all the libraries created.
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| Contributor(s) |
Celen I, Doh JH, Sabanayagam CR |
| Citation missing |
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| Submission date |
Sep 12, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Irem Celen |
| E-mail(s) |
irem@udel.edu
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| Organization name |
University of Delaware
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| Street address |
15 Innovation Way
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19711 |
| Country |
USA |
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| Platforms (1) |
| GPL18245 |
Illumina HiSeq 2500 (Caenorhabditis elegans) |
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| Samples (70)
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| Relations |
| BioProject |
PRJNA406964 |
| SRA |
SRP117357 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE103775_RAW.tar |
4.2 Mb |
(http)(custom) |
TAR (of BED, BROADPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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