|
| Status |
Public on Aug 02, 2016 |
| Title |
Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental to our current view of chromatin structure and function. It allows genome-wide mapping of histone marks, which demarcate biologically relevant domains. However, ChIP-seq is an ensemble measurement reporting the average occupancy of individual marks in a cell population. Consequently, our understanding of the combinatorial nature of chromatin states relies almost exclusively on correlation between the genomic distributions of individual marks. Here, we report the development of Combinatorial-iChIP to determine the genome-wide co-occurrence of histone marks at single nucleosome resolution. By comparing to null model, we show that certain combinations of overlapping marks (H3K36me3 and H3K79me3) co-occur more frequently than expected by chance, while others (H3K4me3 and H3K36me3) do not, reflecting differences in the underlying chromatin pathways. We further use combinatorial-iChIP to illuminate aspects of the Set2-RPD3S pathway. This approach promises to improve our understanding of the combinatorial complexity of chromatin.
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| |
|
| Overall design |
Combinatorial iChIP in yeast.
|
| |
|
| Contributor(s) |
Ronen S, Roee L, Hava W, Ayelet R, Nir F |
| Citation(s) |
27496019 |
| |
| Submission date |
Jul 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nir Friedman |
| E-mail(s) |
nir@cs.huji.ac.il
|
| Organization name |
The Hebrew University of Jerusalem
|
| Department |
School of Engineering
|
| Street address |
Givat Ram
|
| City |
Jerusalem |
| ZIP/Postal code |
9190401 |
| Country |
Israel |
| |
|
| Platforms (1) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
|
| Samples (180)
|
|
| Relations |
| BioProject |
PRJNA328453 |
| SRA |
SRP078243 |
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