ArticleProceedings of the National Academy of Sciences of the United States of America2010
Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 25 citations in OpenAlex.
- Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage.iScience · 2024Article
- Tissue-wide coordination of epithelium-to-neural stem cell transition in the Drosophila optic lobe requires Neuralized.The Journal of cell biology · 2020Article
- BICORN: An R package for integrative inference of de novo cis-regulatory modules.Scientific reports · 2020Article
- Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals.PLoS computational biology · 2018Article
- Lateral inhibition: Two modes of non-autonomous negative autoregulation by neuralized.PLoS genetics · 2018Article
- MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis.Nucleic acids research · 2016Article
- Comparison between Timelines of Transcriptional Regulation in Mammals, Birds, and Teleost Fish Somitogenesis.PloS one · 2016Article
- Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation.Nucleic acids research · 2014Article
- Article
- A general pairwise interaction model provides an accurate description of in vivo transcription factor binding sites.PloS one · 2014Article
- Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization.Genome biology · 2013Article
- Phylogenetic footprinting: a boost for microbial regulatory genomics.Protoplasma · 2012Review
- Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers.Developmental dynamics : an official publication of the American Association of Anatomists · 2012Article
- A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis.PLoS genetics · 2012Article
- Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.Nucleic acids research · 2011Article
- A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation.BMC plant biology · 2011Article
- Linking specification to differentiation: From proneural genes to the regulation of ciliogenesis.FlyArticle
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell fate determination depends in part on the establishment of specific transcriptional programs of gene expression. These programs result from the interpretation of the genomic cis-regulatory information by sequence-specific factors. Decoding this information in sequenced genomes is an important issue. Here, we developed statistical analysis tools to computationally identify the cis-regulatory elements that control gene expression in a set of coregulated genes. Starting with a small number of validated and/or predicted cis-regulatory modules (CRMs) in a reference species as a training set, but with no a priori knowledge of the factors acting in trans, we computationally predicted transcription factor binding sites (TFBSs) and genomic CRMs underlying coregulation. This method was applied to the gene expression program active in Drosophila melanogaster sensory organ precursor cells (SOPs), a specific type of neural progenitor cells. Mutational analysis showed that four, including one newly characterized, out of the five top-ranked families of predicted TFBSs were required for SOP-specific gene expression. Additionaly, 19 out of the 29 top-ranked predicted CRMs directed gene expression in neural progenitor cells, i.e., SOPs or larval brain neuroblasts, with a notable fraction active in SOPs (11/29). We further identified the lola gene as the target of two SOP-specific CRMs and found that the lola gene contributed to SOP specification. The statistics and phylogeny-based tools described here can be more generally applied to identify the cis-regulatory elements of specific gene regulatory networks in any family of related species with sequenced genomes.
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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.