ArticleMolecular systems biology2010
Dynamic CRM occupancy reflects a temporal map of developmental progression.
Article in Molecular systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 48 citations in OpenAlex.
- Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function.Nature structural & molecular biology · 2024Article
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- Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function.bioRxiv : the preprint server for biology · 2023Article
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
- Extremely rapid and reversible optogenetic perturbation of nuclear proteins in living embryos.Developmental cell · 2021Article
- Accurate prediction ofNAR genomics and bioinformatics · 2021Article
- Cooperative binding between distant transcription factors is a hallmark of active enhancers.Molecular cell · 2021Article
- Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated.Development (Cambridge, England) · 2020Article
- A map of direct TF-DNA interactions in the human genome.Nucleic acids research · 2019Article
- A transcription factor collective defines the HSN serotonergic neuron regulatory landscape.eLife · 2018Article
- Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity.eLife · 2017Article
- Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers.BMC medical genomics · 2017Article
- Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development.Genetics · 2017Article
- Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.PLoS computational biology · 2016Article
- Putting chromatin in its place: the pioneer factor NeuroD1 modulates chromatin state to drive cell fate decisions.The EMBO journal · 2016Article
- Absence of a simple code: how transcription factors read the genome.Trends in biochemical sciences · 2014Review
- Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm.The EMBO journal · 2013Article
- Transcription factor and chromatin features predict genes associated with eQTLs.Nucleic acids research · 2013Article
- Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data.BMC systems biology · 2013Article
- Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning.PLoS genetics · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Development is driven by tightly coordinated spatio-temporal patterns of gene expression, which are initiated through the action of transcription factors (TFs) binding to cis-regulatory modules (CRMs). Although many studies have investigated how spatial patterns arise, precise temporal control of gene expression is less well understood. Here, we show that dynamic changes in the timing of CRM occupancy is a prevalent feature common to all TFs examined in a developmental ChIP time course to date. CRMs exhibit complex binding patterns that cannot be explained by the sequence motifs or expression of the TFs themselves. The temporal changes in TF binding are highly correlated with dynamic patterns of target gene expression, which in turn reflect transitions in cellular function during different stages of development. Thus, it is not only the timing of a TF's expression, but also its temporal occupancy in refined time windows, which determines temporal gene expression. Systematic measurement of dynamic CRM occupancy may therefore serve as a powerful method to decode dynamic changes in gene expression driving developmental progression.
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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.