ArticleMolecular systems biology2009
Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression.
Article in Molecular systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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Who cites it
22 citing papers in PubMed, 39 citations in OpenAlex.
- The structure is the message: Preserving experimental context through tensor decomposition.Cell systems · 2024Review
- Global early replication disrupts gene expression and chromatin conformation in a single cell cycle.Genome biology · 2022Article
- Point centromere activity requires an optimal level of centromeric noncoding RNA.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- DNA replication timing influences gene expression level.The Journal of cell biology · 2017Article
- Tensor factorization toward precision medicine.Briefings in bioinformatics · 2017Article
- TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors.Science signaling · 2016Article
- Article
- Genome-wide replication landscape of Candida glabrata.BMC biology · 2015Article
- Subgraph augmented non-negative tensor factorization (SANTF) for modeling clinical narrative text.Journal of the American Medical Informatics Association : JAMIA · 2015Article
- Article
- Article
- Maintaining replication origins in the face of genomic change.Genome research · 2012Article
- On a fundamental structure of gene networks in living cells.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Cytomegalovirus replicon-based regulation of gene expression in vitro and in vivo.PLoS pathogens · 2012Article
- Article
- OriDB, the DNA replication origin database updated and extended.Nucleic acids research · 2012Article
- Cruciform structures are a common DNA feature important for regulating biological processes.BMC molecular biology · 2011Review
- Defining the replication program through the chromatin landscape.Critical reviews in biochemistry and molecular biology · 2011Review
- Convergence of logic of cellular regulation in different premalignant cells by an information theoretic approach.BMC systems biology · 2011Article
- A higher-order generalized singular value decomposition for comparison of global mRNA expression from multiple organisms.PloS one · 2011Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
This report provides a global view of how gene expression is affected by DNA replication. We analyzed synchronized cultures of Saccharomyces cerevisiae under conditions that prevent DNA replication initiation without delaying cell cycle progression. We use a higher-order singular value decomposition to integrate the global mRNA expression measured in the multiple time courses, detect and remove experimental artifacts and identify significant combinations of patterns of expression variation across the genes, time points and conditions. We find that, first, approximately 88% of the global mRNA expression is independent of DNA replication. Second, the requirement of DNA replication for efficient histone gene expression is independent of conditions that elicit DNA damage checkpoint responses. Third, origin licensing decreases the expression of genes with origins near their 3' ends, revealing that downstream origins can regulate the expression of upstream genes. This confirms previous predictions from mathematical modeling of a global causal coordination between DNA replication origin activity and mRNA expression, and shows that mathematical modeling of DNA microarray data can be used to correctly predict previously unknown biological modes of regulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.