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| Status |
Public on Oct 07, 2005 |
| Title |
H2A.Z marks the 5' end of genes |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
In S. cerevisiae, histone variant H2A.Z is deposited in euchromatin at the flanks of silent heterochromatin to prevent its ectopic spread. The degree to which H2A.Z is found and functions elsewhere is unknown. Here we show that H2A.Z nucleosomes are found at promoter regions of nearly all genes in euchromatin. They generally occur as two positioned nucleosomes that flank a nucleosome-free region (NFR) that contains the transcription start site. Astonishingly, enrichment at 5’ ends is independent of transcriptional state as it is observed not only at actively transcribed genes, but also at inactive loci. Mutagenesis of a typical promoter revealed a 22 bp segment of DNA sufficient to program formation of a NFR flanked by two H2A.Z nucleosomes. This segment contains a binding site of the Myb-related protein Reb1 and an adjacent dT:dA tract. Efficient deposition of H2A.Z is further promoted by a specific pattern of histone H3 and H4 tail acetylation and the bromodomain protein Bdf1, a component of the Swr1 complex that deposits H2A.Z. These data define DNA- and histone-based mechanisms by which dividing cells define the 5’ ends of genes and preserve their euchromatic state in the absence of transcription.
Keywords: ChIP-chip
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| Overall design |
In mid-log phase S. cerevisiae, we performed ChIP-chip on Htz1 (the histone variant H2A.Z) and compared its enrichment levels within the genome based on nucleosome position data in series GSE2563. Each TLAD-amplified ChIP sample was labeled with Cy5 and hybridized against Cy3-labeled, TLAD-amplified input on oligonucleotide tiling arrays. Five replicates (2 biological, 3 technical) were performed .
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| Contributor(s) |
Raisner RM, Hartley PD, Meneghini MD, Bao MZ, Liu CL, Schreiber SL, Rando OJ, Madhani HD |
| Citation(s) |
16239142 |
| |
| Submission date |
Oct 04, 2005 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Oliver Rando |
| E-mail(s) |
Oliver.Rando@umassmed.edu
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| Phone |
508-856-8879
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| Organization name |
UMass Medical School
|
| Street address |
364 Plantation St.
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605-4321 |
| Country |
USA |
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| Platforms (1) |
| GPL2626 |
yeast_nucleosome_positioning_microarray 10+ |
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| Samples (5)
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| GSM76930 |
H2A.Z Biological Replicate 1 vs input | array 11_130 |
| GSM76931 |
H2A.Z Biological Replicate 2 vs input | array 11_127 |
| GSM76932 |
H2A.Z Biological Replicate 2 vs input | array 11_155 |
| GSM76933 |
H2A.Z Biological Replicate 2 vs input | array 11_156 |
| GSM76934 |
H2A.Z Biological Replicate 1 vs input | array 11_123 |
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| Relations |
| BioProject |
PRJNA93433 |
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