 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 26, 2014 |
| Title |
Nucleosome loss leads to global transcriptional upregulation and genomic instability during yeast replicative aging |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
All eukaryotic cells divide a finite number of times, termed replicative aging, but the reason for this is not clear. Consistent with the decreased total histone protein levels in aged Saccharomyces cerevisiae, which is a cause of aging (1), we find that nucleosome occupancy decreases 50% across the whole genome during replicative aging by spike-in controlled MNase sequencing. Nucleosomes become fuzzier or move to sequences predicted to better accommodate histone octamers. All yeast genes are induced during aging. Genes that are repressed in young cells are most induced, accompanied by nucleosome loss from their promoters that have unique chromatin organization. Contrary to the loss of mitochondrial function during aging, mitochondrial DNA content increases and unprecedented levels of large-scale chromosomal alterations and increased retrotransposition are observed.
|
| |
|
| Overall design |
Mnase-Seq experiments were carried out for young yeast, old yeast, and old yeast with histone over expression, 3 replicates were done for each category. RNA-Seq were carried out for the same categories of yeast cells but with 2 replicates for each. Genome-Seq were done for the young and old yeast with 2 replicates for each.
|
| |
|
| Contributor(s) |
Hu Z, Chen K, Xia Z, Chavez M, Seol J, Li W, Tyler JK |
| Citation(s) |
24532716 |
| Submission date |
May 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
kaifu chen |
| E-mail(s) |
kaifuc@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor plaza, suite 450A
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
|
| Samples (19)
|
| GSM1143089 |
[MNase-Seq] Young yeast nucleosome replicate1 |
| GSM1143090 |
[MNase-Seq] Young yeast nucleosome replicate2 |
| GSM1143091 |
[MNase-Seq] Young yeast nucleosome replicate3 |
| GSM1143092 |
[MNase-Seq] Old yeast with histone over expression, nucleosome replicate1 |
| GSM1143093 |
[MNase-Seq] Old yeast with histone over expression, nucleosome replicate2 |
| GSM1143094 |
[MNase-Seq] Old yeast with histone over expression, nucleosome replicate3 |
| GSM1143095 |
[MNase-Seq] Old yeast nucleosome replicate1 |
| GSM1143096 |
[MNase-Seq] Old yeast nucleosome replicate2 |
| GSM1143097 |
[MNase-Seq] Old yeast nucleosome replicate3 |
| GSM1143098 |
[Genome-Seq] Young yeast genome replicate1 (MNase-Seq input) |
| GSM1143099 |
[Genome-Seq] Young yeast genome replicate2 (MNase-Seq input) |
| GSM1143100 |
[Genome-Seq] Old yeast genome replicate1 (MNase-Seq input) |
| GSM1143101 |
[Genome-Seq] Old yeast genome replicate2 (MNase-Seq input) |
| GSM1143102 |
[RNA-Seq] Young yeast RNA replicate1 |
| GSM1143103 |
[RNA-Seq] Young yeast RNA replicate2 |
| GSM1143104 |
[RNA-Seq] Old yeast with histone over expression, RNA replicate1 |
| GSM1143105 |
[RNA-Seq] Old yeast with histone over expression, RNA replicate2 |
| GSM1143106 |
[RNA-Seq] Old yeast RNA replicate1 |
| GSM1143107 |
[RNA-Seq] Old yeast RNA replicate2 |
|
| Relations |
| BioProject |
PRJNA203300 |
| SRA |
SRP022854 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47023_RAW.tar |
726.4 Mb |
(http)(custom) |
TAR (of WIG) |
| GSE47023_expression.txt.gz |
167.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...