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Series GSE210821 Query DataSets for GSE210821
Status Public on Aug 12, 2022
Title Evaluation of the impact of chromosomal inversions on replication origin usage in fission yeast
Organism Schizosaccharomyces pombe
Experiment type Expression profiling by array
Summary Eukaryotic DNA replication is regulated by conserved mechanisms that bring about a spatial and temporal organization in which distinct genomic domains are copied at characteristic times during S phase. Although this replication program has been closely linked with genome architecture, we still do not understand key aspects of how chromosomal context modulates the activity of replication origins. To address this question, we have exploited models that combine engineered genomic rearrangements with the unique replication programs of post-quiescence and pre-meiotic S phases. Our results demonstrate that large-scale inversions surprisingly do not affect cell proliferation and meiotic progression, despite inducing a restructuring of replication domains on each rearranged chromosome. Remarkably, these alterations in the organization of DNA replication are entirely due to changes in the positions of existing origins along the chromosome, as their efficiencies remain virtually unaffected genome wide. However, we identified striking alterations in origin firing proximal to the fusion points of each inversion, suggesting that the immediate chromosomal neighborhood of an origin is a crucial determinant of its activity. Interestingly, the impact of genome reorganization on replication initiation is highly comparable in the post-quiescent and pre-meiotic S phases, despite the differences in DNA metabolism in these two physiological states. Our findings therefore shed new light on how origin selection and the replication program are governed by chromosomal architecture.
Genes 2022, 13(7), 1244; https://doi.org/10.3390/genes13071244
 
Overall design Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase. Two distinct chromosomal inversions were analyzed, each compared to an accompanying control (pre-arrangement) strain. Two biological repeats were performed and averaged for each experiment; dye-swaps were performed and averaged for each biological repeat. Each chromosomal inversion and its control were analyzed for origin usage in post-quiescence and pre-meiotic S phase. A total of 16 experiments were performed, giving rise to 32 datasets.
 
Contributor(s) Wu PJ
Citation(s) 35886027
Submission date Aug 09, 2022
Last update date Nov 14, 2022
Contact name Pei-Yun Jenny Wu
E-mail(s) pei-yun.wu@ibgc.cnrs.fr
Organization name Institute of Biochemistry and Cellular Genetics
Lab CNRS UMR 5095
Street address 1 Rue Camille Saint Saens
City Bordeaux
ZIP/Postal code 33077
Country France
 
Platforms (1)
GPL16235 Agilent-015424 S. pombe Whole Genome ChIP-on-Chip Microarray 4x44K (Probe Name version - A_93_Pnnnn probes)
Samples (32)
GSM6438732 Origin mapping of the control strain for the chromosome I rearrangement, post-quiescence, replicate 1, dye-swap 1
GSM6438733 Origin mapping of the control strain for the chromosome I rearrangement, post-quiescence, replicate 1, dye-swap 2
GSM6438734 Origin mapping of the control strain for the chromosome I rearrangement, post-quiescence, replicate 2, dye-swap 1
Relations
BioProject PRJNA867670

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
GSE210821_Analyzed_data.txt.gz 1.7 Mb (ftp)(http) TXT
GSE210821_RAW.tar 147.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data are available on Series record

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