ArticleProceedings of the National Academy of Sciences of the United States of America2009
DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 28 citations in OpenAlex.
- Roles of the NFI/CTF gene family in transcription and development: update 2025.Academia biology · 2025Article
- The cecropin-prophenoloxidase regulatory mechanism is a cross-species physiological function in mosquitoes.iScience · 2022Article
- Nuclear factor I-C disrupts cellular homeostasis between autophagy and apoptosis via miR-200b-Ambra1 in neural tube defects.Cell death & disease · 2021Article
- The plant-parasitic cyst nematode effector GLAND4 is a DNA-binding protein.Molecular plant pathology · 2018Article
- Nutrient-DrivenFrontiers in endocrinology · 2018Article
- Involvement of cecropin B in the formation of the Aedes aegypti mosquito cuticle.Scientific reports · 2017Article
- Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.Molecular systems biology · 2017Article
- Reverse engineering highlights potential principles of large gene regulatory network design and learning.NPJ systems biology and applications · 2017Article
- Functional analysis of structurally related soybean GmWRKY58 and GmWRKY76 in plant growth and development.Journal of experimental botany · 2016Article
- Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution.Genome biology and evolution · 2015Article
- Transcription Factor Activity Mapping of a Tissue-SpecificCell systems · 2015Article
- Principles of allosteric interactions in cell signaling.Journal of the American Chemical Society · 2014Review
- Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites.Biophysical journal · 2013Article
- Transcriptional regulation of gene expression in C. elegans.WormBook : the online review of C. elegans biology · 2013Review
- Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2012Article
- Fast, sensitive discovery of conserved genome-wide motifs.Journal of computational biology : a journal of computational molecular cell biology · 2012Article
- Seeing elegance in gene regulatory networks of the worm.Current opinion in genetics & development · 2011Review
- Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex.PLoS genetics · 2011Article
- Gene-centered regulatory network mapping.Methods in cell biology · 2011Review
- Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
The conserved nuclear factor I (NFI) family of transcription factors is unique to animals and essential for mammalian development. The Caenorhabditis elegans genome encodes a single NFI family member, whereas vertebrate genomes encode 4 distinct NFI protein subtypes (A, B, C, and X). NFI-1-deficient worms exhibit abnormalities, including reduced lifespan, defects in movement and pharyngeal pumping, and delayed egg-laying. To explore the functional basis of these phenotypes, we sought to comprehensively identify NFI-1-bound loci in C. elegans. We first established NFI-1 DNA-binding specificity using an in vitro DNA-selection strategy. Analysis yielded a consensus motif of TTGGCA(N)(3)TGCCAA, which occurs 586 times in the genome, a 100-fold higher frequency than expected. We next asked which sites were occupied by NFI-1 in vivo by performing chromatin immunoprecipitation of NFI-1 followed by microarray hybridization. Only 55 genomic locations were identified, an unexpectedly small target set. In vivo NFI-1 binding sites tend to be upstream of genes involved in core cellular processes, such as chromatin remodeling, mRNA splicing, and translation. Remarkably, 59 out of 70 (84%) of the C. briggsae orthologs of the identified targets contain conserved NFI binding sites in their promoters. These experiments provide a foundation for understanding how NFI-1 is recruited to unexpectedly few in vivo sites to perform its developmental functions, despite a vast over-representation of its binding motif.
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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.