ArticleGenome research2005
Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics.
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 13 papers.
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Who cites it
13 citing papers in PubMed, 31 citations in OpenAlex.
- Adaptive Response ofJournal of fungi (Basel, Switzerland) · 2022Article
- A Biological Inventory of Prophages inFrontiers in microbiology · 2020Article
- A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae.BMC genomics · 2016Article
- Reduced Ssy1-Ptr3-Ssy5 (SPS) signaling extends replicative life span by enhancing NAD+ homeostasis in Saccharomyces cerevisiae.The Journal of biological chemistry · 2015Article
- Defining the plasticity of transcription factor binding sites by Deconstructing DNA consensus sequences: the PhoP-binding sites among gamma/enterobacteria.PLoS computational biology · 2010Article
- SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics.BMC bioinformatics · 2008Article
- Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila.BMC bioinformatics · 2007Article
- Comparative analysis of regulatory motif discovery tools for transcription factor binding sites.Genomics, proteomics & bioinformatics · 2007Article
- Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.BMC bioinformatics · 2006Article
- Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.BMC bioinformatics · 2006Article
- Linking DNA-binding proteins to their recognition sequences by using protein microarrays.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Phylogeny based discovery of regulatory elements.BMC bioinformatics · 2006Article
- Practical strategies for discovering regulatory DNA sequence motifs.PLoS computational biology · 2006Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Completing the annotation of a genome sequence requires identifying the regulatory sequences that control gene expression. To identify these sequences, we developed an algorithm that searches for short, conserved sequence motifs in the genomes of related species. The method is effective in finding motifs de novo and for refining known regulatory motifs in Saccharomyces cerevisiae. We tested one novel motif prediction of the algorithm and found it to be the binding site of Stp2; it is significantly different from the previously predicted Stp2 binding site. We show that Stp2 physically interacts with this sequence motif, and that stp2 mutations affect the expression of genes associated with the motif. We demonstrate that the Stp2 binding site also interacts genetically with Stp1, a regulator of amino acid permease genes and, with Sfp1, a key regulator of cell growth. These results illuminate an important transcriptional circuit that regulates cell growth through external nutrient uptake.
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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.