E-MTAB-1409 - ChIP-chip by array of Saccharomyces cerevisiae to understand the dynamics of yeast histone H2A and H2B phosphorylation in response to a double-strand break

Status
Released on 15 December 2013, last updated on 3 May 2014
Organism
Saccharomyces cerevisiae
Samples (16)
Array (1)
Protocols (7)
Description
In Saccharomyces cerevisiae, a single double-strand break (DSB) triggers extensive phosphorylation of histone H2A (known as gammaH2AX) over 50 kb on either side of the DSB. This modification is carried out by either of yeast’s checkpoint kinases, the ATM homolog, Tel1, or the ATR homolog, Mec1. In G1-arrested cells, where there is very little 5’ to 3’ processing of DSB ends, only Tel1 promotes this modification. We have recently described a second modification gammaH2B - the phosphorylation of the C terminal T129 locus of histone H2B which is also carried out by both Mec1 and Tel1 kinases. To understand in detail how gamma-H2AX and gamma-H2B spread along the chromosome from a DSB we have undertaken a high-density analysis of their occupancy where there is a DSB on three different chromosomes. gamma-H2AX and gamma-H2B modifications are similar, but there is a marked absence of gamma-H2B near telomeres. We find that there is reduced gamma-H2AX and gamma-H2B modification over strongly transcribed regions, even taking into account the reduced histone occupancy of these genes. When transcription of the galactose-regulated genes GAL1, GAL10, GAL7 are turned off by the addition of glucose, gamma-H2AX is restored within 5 min; when these genes are again induced, gamma-H2AX is rapidly lost. Regions more distal to the GAL genes have markedly reduced gamma-H2AX levels that rise rapidly when transcription is repressed, suggesting that transcription acts as a barrier to the propagation of gamma-H2AX away from the DSB. The restoration of gamma-H2AX in transcribed regions can be carried out by either Mec1 or Tel1, even 7 h after break induction, suggesting that Tel1 remains associated with damaged chromosomes for an extended time. In addition, we show that gamma-H2AX can be transferred in trans, to regions unlinked to the DSB that lie in close proximity the DSB. Specifically, if a DSB is generated 14 kb from CEN2, gamma-H2AX is transferred to regions around all the other centromeres, in keeping with observed close proximity of all centromere-adjacent chromosome arms. This transfer can be observed even in the absence of formaldehyde crosslinking of the samples.
Experiment types
ChIP-chip by array, binding site identification, compound treatment, in vivo, strain or line
Contact
Citation
Dynamics of yeast histone H2A and H2B phosphorylation in response to a double-strand break. Cheng-Sheng Lee, Kihoon Lee, Gaelle Legube, James E Haber. Nature Structural and Molecular Biology   (2013)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-1409.idf.txt
Sample and data relationshipE-MTAB-1409.sdrf.txt
Raw data (2)E-MTAB-1409.raw.1.zip, E-MTAB-1409.raw.2.zip
Processed data (1)E-MTAB-1409.processed.1.zip
Array designA-GEOD-6476.adf.txt
Links