ArticleGenome research2007
Identification of muscle-specific regulatory modules in Caenorhabditis elegans.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
- A single-copy knockin translating ribosome immunoprecipitation toolkit for tissue-specific profiling of actively translated mRNAs inCell reports methods · 2023Article
- MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks.PloS one · 2023Article
- Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration.Frontiers in molecular neuroscience · 2022Article
- Genome-wide chromatin accessibility analyses provide a map for enhancing optic nerve regeneration.Scientific reports · 2021Article
- The Transcriptional Regulator SnoN Promotes the Proliferation of Cerebellar Granule Neuron Precursors in the Postnatal Mouse Brain.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2019Article
- Modeling thePeerJ · 2017Article
- Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.BMC bioinformatics · 2016Article
- Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.eLife · 2015Article
- Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation.Nucleic acids research · 2014Article
- A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster.PloS one · 2014Article
- A regulatory module controlling pharyngeal development and function in Caenorhabditis elegans.Genetics · 2012Article
- Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2012Article
- The Caenorhabditis elegans paxillin orthologue, PXL-1, is required for pharyngeal muscle contraction and for viability.Molecular biology of the cell · 2011Article
- Scaffolding a Caenorhabditis nematode genome with RNA-seq.Genome research · 2010Article
- Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans.Nucleic acids research · 2010Article
- Computational design and application of endogenous promoters for transcriptionally targeted gene therapy for rheumatoid arthritis.Molecular therapy : the journal of the American Society of Gene Therapy · 2009Article
- Transcription factor site dependencies in human, mouse and rat genomes.BMC bioinformatics · 2009Article
- Modeling the quantitative specificity of DNA-binding proteins from example binding sites.PloS one · 2009Article
- Information flow analysis of interactome networks.PLoS computational biology · 2009Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Transcriptional regulation is the major regulatory mechanism that controls the spatial and temporal expression of genes during development. This is carried out by transcription factors (TFs), which recognize and bind to their cognate binding sites. Recent studies suggest a modular organization of TF-binding sites, in which clusters of transcription-factor binding sites cooperate in the regulation of downstream gene expression. In this study, we report our computational identification and experimental verification of muscle-specific cis-regulatory modules in Caenorhabditis elegans. We first identified a set of motifs that are correlated with muscle-specific gene expression. We then predicted muscle-specific regulatory modules based on clusters of those motifs with characteristics similar to a collection of well-studied modules in other species. The method correctly identifies 88% of the experimentally characterized modules with a positive predictive value of at least 65%. The prediction accuracy of muscle-specific expression on an independent test set is highly significant (P<0.0001). We performed in vivo experimental tests of 12 predicted modules, and 10 of those drive muscle-specific gene expression. These results suggest that our method is highly accurate in identifying functional sequences important for muscle-specific gene expression and is a valuable tool for guiding experimental designs.
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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.