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Series GSE74090 Query DataSets for GSE74090
Status Public on Aug 25, 2016
Title Dynamics of chromatin maturation after genome replication
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Replication of the eukaryotic genome occurs in the context of chromatin, a nucleoprotein packaging state consisting of repeating nucleosomes. Chromatin is commonly thought to carry epigenetic information from one generation to the next, although it is unclear how such information survives the disruptions of nucleosomal architecture that occur during genomic replication. Here, we sought to directly measure a key aspect of chromatin structure dynamics during replication – how rapidly nucleosome positions are established on the newly-replicated daughter genomes. By isolating newly-synthesized DNA marked with the nucleotide analogue EdU, we characterize nucleosome positions on both daughter genomes of budding yeast during a time course of chromatin maturation. We find that nucleosomes rapidly adopt their mid log positions at highly-transcribed genes, and that this process was impaired upon treatment with the transcription inhibitor thiolutin, consistent with a role for transcription in positioning nucleosomes in vivo. Additionally, experiments in the Hir1Δ background reveal a role for HIR in nucleosome spacing. Using strand-specific EdU libraries, we characterize nucleosome positions on the leading and lagging strand daughter genomes, uncovering differences in chromatin maturation dynamics between the two daughter genomes at hundreds of genes. Our data define the maturation dynamics of newly-replicated chromatin, and support a role for transcription in sculpting the chromatin template.
 
Overall design We have mapped changes in nucleosome positions on newly replicated DNA in a timecourse after genome replication. We have used Micrococcal Nuclease footprinting of cross linked chromatin to determine nucleosome positions and EdU (ethylene deoxy uridine) to mark nascent DNA strands. EdU incorporated into nascent DNA strands was biotinylated with Click chemistry and nascent DNA strand fragments were subsequently isolated using Streptavidin coated magnetic beads.
 
Contributor(s) Vasseur P, Tonazzini S, Ziane R, Camsses A, Radman-Livaja M, Rando O
Citation(s) 27568571
Submission date Oct 16, 2015
Last update date Jun 04, 2019
Contact name Marta Radman-Livaja
E-mail(s) mrl5374@gmail.com
Phone +33434359667
Organization name CNRS
Department IGMM
Street address 1919 route de Mende
City Montpellier
ZIP/Postal code 34293
Country France
 
Platforms (3)
GPL9134 Illumina Genome Analyzer (Saccharomyces cerevisiae)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (93)
GSM1909510 Nascent DNA S-phase time course 1
GSM1909511 Nascent DNA S-phase time course 2
GSM1909512 Nascent DNA S-phase time course 3
Relations
BioProject PRJNA298975
SRA SRP064904

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE74090_CHD1D_total_tss_aligned.txt.gz 3.5 Mb (ftp)(http) TXT
GSE74090_IOC3D_total_tss_aligned.txt.gz 3.0 Mb (ftp)(http) TXT
GSE74090_PC_20_10_EdU-tss_aligned.txt.gz 32.2 Mb (ftp)(http) TXT
GSE74090_PC_20_10_EdU_replicate_tss_aligned.txt.gz 22.4 Mb (ftp)(http) TXT
GSE74090_PC_5_5_EdU_+-Thiolutin_input_tss_aligned.txt.gz 59.0 Mb (ftp)(http) TXT
GSE74090_PC_5_5_EdU_+-Thiolutin_tss_aligned.txt.gz 30.5 Mb (ftp)(http) TXT
GSE74090_PC_5_5_EdU_CHD1D_replicate_tss_aligned.txt.gz 27.5 Mb (ftp)(http) TXT
GSE74090_PC_5_5_EdU_CHD1D_tss_aligned.txt.gz 27.5 Mb (ftp)(http) TXT
GSE74090_PC_5_5_EdU_IOC3D_tss_aligned.txt.gz 28.4 Mb (ftp)(http) TXT
GSE74090_PC_5_5_EdU_input2_HIR1D_replicates12_tss_aligned.txt.gz 88.5 Mb (ftp)(http) TXT
GSE74090_PC_5_5_EdU_replicate_tss_aligned.txt.gz 23.3 Mb (ftp)(http) TXT
GSE74090_PC_5_5_input_HIR1D_tss_aligned.txt.gz 15.9 Mb (ftp)(http) TXT
GSE74090_Sync_EdU_input_tss_aligned.txt.gz 31.3 Mb (ftp)(http) TXT
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