ArticleNucleic acids research2014
Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
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- A TFEB-TGFβ axis systemically regulates diapause, stem cell resilience and protects against a senescence-like state.Nature aging · 2025Article
- Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis in C. elegans.Development (Cambridge, England) · 2024Article
- Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity inNAR genomics and bioinformatics · 2024Article
- Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis inbioRxiv : the preprint server for biology · 2024Article
- A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans.Nature communications · 2024Article
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- A Functional Variant Alters the Binding ofAnimals : an open access journal from MDPI · 2023Article
- Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in Caenorhabditis elegans.Genetics · 2023Article
- Targeted DamID inScience advances · 2022Article
- Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources.BMC bioinformatics · 2021Article
- Gene bashing ofmicroPublication biology · 2020Article
- Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences.Journal of visualized experiments : JoVE · 2019Article
- Gene-Centered Yeast One-Hybrid Assays.Cold Spring Harbor protocols · 2016Article
- Negative Glucocorticoid Response-Like Element from the First Intron of the Chicken Growth Hormone Gene Represses Gene Expression in the Rat Pituitary Tumor Cell Line.International journal of molecular sciences · 2016Article
- A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions.Molecular systems biology · 2016Article
- Glutathione reductase gsr-1 is an essential gene required for Caenorhabditis elegans early embryonic development.Free radical biology & medicine · 2016Article
- Article
- The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites.BMC genomics · 2014Article
- Transgene-mediated co-suppression of DNA topoisomerase-1 gene in Caenorhabditis elegans.International journal of biochemistry and molecular biology · 2014Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
Gene expression is controlled through the binding of transcription factors (TFs) to regulatory genomic regions. First introns are longer than other introns in multiple eukaryotic species and are under selective constraint. Here we explore the importance of first introns in TF binding in the nematode Caenorhabditis elegans by combining computational predictions and experimentally derived TF-DNA interaction data. We found that first introns of C. elegans genes, particularly those for families enriched in long first introns, are more conserved in length, have more conserved predicted TF interactions and are bound by more TFs than other introns. We detected a significant positive correlation between first intron size and the number of TF interactions obtained from chromatin immunoprecipitation assays or determined by yeast one-hybrid assays. TFs that bind first introns are largely different from those binding promoters, suggesting that the different interactions are complementary rather than redundant. By combining first intron and promoter interactions, we found that genes that share a large fraction of TF interactions are more likely to be co-expressed than when only TF interactions with promoters are considered. Altogether, our data suggest that C. elegans gene regulation may be additive through the combined effects of multiple regulatory regions.
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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.