ArticleGenome research2006
Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 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.
The trial behind it
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
108 citing papers in PubMed.
- REST elevation-dependent chromatin remodeling and alternative Grk6 transcript synthesis hyperactivates Cxcr4-Sdf1 signaling in cerebellar granule cell progenitors.bioRxiv : the preprint server for biology · 2025Article
- Genome-Wide Silencer Screening Reveals Key Silencer Modulating Reprogramming Efficiency in Mouse Induced Pluripotent Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- REST Is Restless in Neuronal and Non-Neuronal Virus Infections: An In Silico Analysis-Based Perspective.Viruses · 2025Review
- Estrogen receptor alpha mediated repression of PRICKLE1 destabilizes REST and promotes uterine fibroid pathogenesis.bioRxiv : the preprint server for biology · 2024Article
- Analysis of REST binding sites with canonical and non-canonical motifs in human cell lines.BMC medical genomics · 2024Article
- REST Is Not Resting: REST/NRSF in Health and Disease.Biomolecules · 2023Review
- DNA methylation alterations at RE1-silencing transcription factor binding sites and their flanking regions in cancer.Clinical epigenetics · 2023Article
- Identification of non-coding silencer elements and their regulation of gene expression.Nature reviews. Molecular cell biology · 2023Review
- Genome-wide Association Studies of REST Gene Associated Neurological Diseases/traits with Related Single Nucleotide Polymorphisms.Current neurovascular research · 2023Article
- Why do tumor-infiltrating lymphocytes have variable efficacy in the treatment of solid tumors?Frontiers in immunology · 2022Review
- The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2021Article
- Neuroinflammation induces synaptic scaling through IL-1β-mediated activation of the transcriptional repressor REST/NRSF.Cell death & disease · 2021Article
- Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Transcriptional regulation of adult neural stem/progenitor cells: tales from the subventricular zone.Neural regeneration research · 2020Review
- Possible mechanisms of lycopene amelioration of learning and memory impairment in rats with vascular dementia.Neural regeneration research · 2020Article
- Expression of Repressor Element 1 Silencing Transcription Factor (REST) in Serotonin Neurons in the Adult Male Nile Tilapia (Frontiers in neuroanatomy · 2020Article
- REST-DRD2 mechanism impacts glioblastoma stem cell-mediated tumorigenesis.Neuro-oncology · 2019Article
- AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification.Nucleic acids research · 2019Article
- Inhibition of the Epigenetic Regulator REST Ameliorates Ischemic Brain Injury.Molecular neurobiology · 2019Article
- Mild Inactivation of RE-1 Silencing Transcription Factor (REST) Reduces Susceptibility to Kainic Acid-Induced Seizures.Frontiers in cellular neuroscience · 2019Article
48 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We constructed and applied an open source informatic framework called Cistematic in an effort to predict the target gene repertoire for transcription factors with large binding sites. Cistematic uses two different evolutionary conservation-filtering algorithms in conjunction with several analysis modules. Beginning with a single conserved and biologically tested site for the neuronal repressor NRSF/REST, Cistematic generated a refined PSFM (position specific frequency matrix) based on conserved site occurrences in mouse, human, and dog genomes. Predictions from this model were validated by chromatin immunoprecipitation (ChIP) followed by quantitative PCR. The combination of transfection assays and ChIP enrichment data provided an objective basis for setting a threshold for membership and rank-ordering a final gene cohort model consisting of 842 high-confidence sites in the human genome associated with 733 genes. Statistically significant enrichment of NRSE-associated genes was found for neuron-specific Gene Ontology (GO) terms and neuronal mRNA expression profiles. A more extensive evolutionary survey showed that NRSE sites matching the PSFM model exist in roughly similar numbers in all fully sequenced vertebrate genomes but are notably absent from invertebrate and protochordate genomes, as is NRSF itself. Some NRSF/REST sites reside in repeats, which suggests a mechanism for both ancient and modern dispersal of NRSEs through vertebrate genomes. Multiple predicted sites are located near neuronal microRNA and splicing-factor genes, and these tested positive for NRSF/REST occupancy in vivo. The resulting network model integrates post-transcriptional and translational controllers, including candidate feedback loops on NRSF and its corepressor, CoREST.
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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.