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| Status |
Public on Oct 11, 2012 |
| Title |
CHD1 remodelers space nucleosomes in vitro and link regular arrays to 5’ ends of genes in S. Pombe |
| Organism |
Schizosaccharomyces pombe |
| Experiment type |
Expression profiling by genome tiling array
Genome binding/occupancy profiling by genome tiling array
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| Summary |
Nucleosome positioning governs access to eukaryotic genomes. Many genes show a stereotypic organisation at their 5’ end: a nucleosome free region just upstream of the transcription start site (TSS) followed by a regular nucleosomal array over the coding region. The determinants for this pervasive pattern are unclear, but nucleosome remodeling ATPases likely are critical. Now we employ deletion mutants to study the role of nucleosome remodeling ATPases in global nucleosome positioning in S. pombe and the corresponding changes in expression patterns. We find a striking evolutionary shift in remodeling enzyme usage between budding and fission yeast. The S. pombe RSC remodeling complex seems not involved in nucleosome positioning, despite its prominent role in S. cerevisiae. While lacking ISWI-type remodelers, S. pombe has two CHD1-type ATPases, Hrp1 and Hrp3. We demonstrate nucleosome spacing activity for both in vitro, and together they are essential for linking regular genic arrays to most TSSs in vivo. Impaired chromatin may but need not lead to changes in transcription. The absence of both causes changed expression for about 20% and increased antisense transcription for 15% of all annotated elements.
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| Overall design |
For RNA expression: total RNA from hrp1D, hrp3D, hrp1Dhrp3D and wt (with actinomycin D) and total RNA from snf21ts at 25C and 34C, snf21ts swr1D at 25C and 34C, pht1D swr1D (without actinomycin D).
For nucleosome mapping: Nucleosomal DNA in pht1Δ swr1Δ mutant, snf21- ts mutant, snf21- ts swr1Δ mutant, mit1Δ mutant, hrp1Δ mutant, hrp3Δ mutant and hrp1Δ hrp3Δ mutant S.pombe vs. Genomic Input DNA in wildtype and mit1Δ mutant S.pombe.
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| Contributor(s) |
Jakubsche J, Persson J, Prasad P, Norman U, Strålfors A, Khorosjutina O, Krietenstein N, Svensson P, Ekwall K, Korber P |
| Citation(s) |
23103765 |
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| Submission date |
Sep 20, 2012 |
| Last update date |
May 27, 2014 |
| Contact name |
Karl Ekwall |
| E-mail(s) |
karl.ekwall@ki.se
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| Phone |
+46 8 6089133
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| Organization name |
Karolinska Inst
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| Street address |
Alfred Nobels Alle 7
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| City |
Stockholm |
| ZIP/Postal code |
S-141 89 |
| Country |
Sweden |
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| Platforms (1) |
| GPL7715 |
[Sp20b_M] Affymetrix S. pombe Tiling 1.0FR Array |
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| Samples (40)
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| Relations |
| BioProject |
PRJNA177319 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41024_RAW.tar |
424.2 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE41024_README.txt |
741 b |
(ftp)(http) |
TXT |
| GSE41024_processed_RNA_data_antisense.txt.gz |
793.2 Kb |
(ftp)(http) |
TXT |
| GSE41024_processed_RNA_data_sense.txt.gz |
793.2 Kb |
(ftp)(http) |
TXT |
| GSE41024_processed_nucleosome_data.txt.gz |
145.3 Mb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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