ArticleGenome research2005
Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 48 citations in OpenAlex.
- Article
- Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend.PeerJ · 2019Article
- Dissecting the complex molecular evolution and expression of polygalacturonase gene family in Brassica rapa ssp. chinensis.Plant molecular biology · 2015Article
- Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities.BMC genomics · 2014Article
- Regulatory architecture determines optimal regulation of gene expression in metabolic pathways.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Integrated genome-scale prediction of detrimental mutations in transcription networks.PLoS genetics · 2011Article
- Mutation rates across budding yeast chromosome VI are correlated with replication timing.Genome biology and evolution · 2011Article
- Epistatic relationships reveal the functional organization of yeast transcription factors.Molecular systems biology · 2010Article
- Finding regulatory DNA motifs using alignment-free evolutionary conservation information.Nucleic acids research · 2010Article
- Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus.Journal of molecular evolution · 2009Article
- COMIT: identification of noncoding motifs under selection in coding sequences.Genome biology · 2009Article
- A catalog of neutral and deleterious polymorphism in yeast.PLoS genetics · 2008Article
- Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects.BMC evolutionary biology · 2008Article
- Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs.BMC genomics · 2008Article
- The evolution of combinatorial gene regulation in fungi.PLoS biology · 2008Article
- Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites.PLoS computational biology · 2008Article
- Sequences conserved by selection across mouse and human malaria species.BMC genomics · 2007Article
- Adaptations to fluctuating selection in Drosophila.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa).International journal of biological sciences · 2007Review
- Housekeeping genes tend to show reduced upstream sequence conservation.Genome biology · 2007Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
To gauge the complexity of gene regulation in yeast, it is essential to know how much promoter sequence is functional. Conservation across species can be a sensitive means of detecting functional sequences, provided that the significance of conservation can be accurately calibrated with the local neutral mutation rate. By analyzing yeast coding and promoter sequences, we find that neutral mutation rates in yeast are uniform genome-wide, in contrast to mammals, where neutral mutation rates vary along chromosomes. We develop an approach that uses this uniform rate to estimate the amount of promoter sequence under purifying selection. This amount is approximately 30%, corresponding to roughly 90 bp for a typical promoter. Furthermore, using a hidden Markov model, we are able to separate each promoter into distinct high and low conservation regions. Known regulatory motifs are strongly biased toward high conservation regions, while low conservation regions have mutation rates similar to that of the neutral background. Certain Gene Ontology groupings of genes (e.g., Carbohydrate Metabolism) have large amounts of high conservation sequence, suggesting complexity in their transcriptional regulation. Others (e.g., RNA Processing) have little high conservation sequence and are likely to be simply regulated. The separation of functionally conserved sequence from the neutral background allows us to estimate the complexity of cis-regulation on a genomic scale.
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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.