|
| Status |
Public on May 13, 2015 |
| Title |
Rate, spectrum, and evolutionary dynamics of spontaneous epimutations |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences.
|
| |
|
| Overall design |
MethylC-seq of Arabidopsis thaliana
|
| |
|
| Contributor(s) |
Schmitz RJ |
| Citation(s) |
25964364, 33023650 |
| |
| Submission date |
Dec 23, 2014 |
| Last update date |
Oct 13, 2020 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
|
| Organization name |
University of Georgia
|
| Department |
Genetics
|
| Street address |
B416 Davison Life Sciences
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
|
| Samples (19)
|
|
| Relations |
| BioProject |
PRJNA271082 |
| SRA |
SRP051507 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE64463_MA1_1_G31_109_r1.txt.gz |
162.1 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_109_r2.txt.gz |
157.6 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_119_r1.txt.gz |
160.6 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_119_r2.txt.gz |
161.5 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_29_r1.txt.gz |
158.6 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_29_r2.txt.gz |
164.9 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_29_r3.txt.gz |
159.2 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_39_r1.txt.gz |
163.8 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_39_r2.txt.gz |
158.6 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_49_r1.txt.gz |
160.9 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_49_r2.txt.gz |
163.2 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_59_r1.txt.gz |
163.1 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_59_r2.txt.gz |
157.4 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_79_r1.txt.gz |
162.9 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_79_r2.txt.gz |
164.6 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_89_r1.txt.gz |
160.7 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_89_r2.txt.gz |
157.8 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_99_r1.txt.gz |
162.1 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_99_r2.txt.gz |
156.6 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G31_99_r3.txt.gz |
164.1 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G32_39_r1.txt.gz |
160.3 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G32_39_r2.txt.gz |
157.9 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G32_49_r1.txt.gz |
157.0 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G32_49_r2.txt.gz |
154.3 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G3_26_r1.txt.gz |
156.7 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G3_87_r1.txt.gz |
161.6 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_1_G3_87_r2.txt.gz |
155.8 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G31_119_r1.txt.gz |
170.5 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G31_119_r2.txt.gz |
156.5 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G31_29_r1.txt.gz |
170.7 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G31_29_r2.txt.gz |
164.2 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G31_49_r1.txt.gz |
170.3 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G31_49_r2.txt.gz |
162.9 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G31_59_r1.txt.gz |
170.1 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G31_59_r2.txt.gz |
162.7 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G3_12_r1.txt.gz |
172.0 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G3_12_r2.txt.gz |
171.8 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G3_19_r1.txt.gz |
169.9 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G3_19_r2.txt.gz |
163.9 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G3_1_r1.txt.gz |
170.2 Mb |
(ftp)(http) |
TXT |
| GSE64463_MA1_2_G3_1_r2.txt.gz |
163.5 Mb |
(ftp)(http) |
TXT |
| GSE64463_RAW.tar |
2.9 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE64463_readme.txt.gz |
317 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
| Processed data are available on Series record |
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