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Spacer sequences separating transcription factor binding motifs set enhancer quality and strength

https://doi.org/10.1101/098830
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.cell.2012.12.009openalex-snapshot
DNA-Binding Specificities of Human Transcription Factors
inferredcites →https://doi.org/10.1016/j.cell.2013.07.034openalex-snapshot
Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites
inferredcites →https://doi.org/10.1016/j.celrep.2012.10.012openalex-snapshot
DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation
inferredcites →https://doi.org/10.1016/j.celrep.2013.03.014openalex-snapshot
Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape
inferredcites →https://doi.org/10.1016/j.cub.2010.03.063openalex-snapshot
A cis-Regulatory Signature in Ascidians and Flies, Independent of Transcription Factor Binding Sites
inferredcites →https://doi.org/10.1016/j.gde.2015.08.009openalex-snapshot
Transcriptional enhancers: functional insights and role in human disease
inferredcites →https://doi.org/10.1016/j.jmb.2008.06.072openalex-snapshot
Crystal Structures of Multiple GATA Zinc Fingers Bound to DNA Reveal New Insights into DNA Recognition and Self-Association by GATA
inferredcites →https://doi.org/10.1016/j.tibs.2014.07.002openalex-snapshot
Absence of a simple code: how transcription factors read the genome
inferredcites →https://doi.org/10.1016/j.tig.2009.08.003openalex-snapshot
Different gene regulation strategies revealed by analysis of binding motifs
inferredcites →https://doi.org/10.1016/j.ydbio.2015.04.023openalex-snapshot
FGF signaling supports Drosophila fertility by regulating development of ovarian muscle tissues
inferredcites →https://doi.org/10.1016/j.ydbio.2015.05.014openalex-snapshot
A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis
inferredcites →https://doi.org/10.1016/j.ymeth.2011.08.010openalex-snapshot
High-throughput protein expression screening and purification in Escherichia coli
inferredcites →https://doi.org/10.1016/s0092-8674(03)00928-0openalex-snapshot
Neural Tissue in Ascidian Embryos Is Induced by FGF9/16/20, Acting via a Combination of Maternal GATA and Ets Transcription Factors
inferredcites →https://doi.org/10.1023/a:1018399711996openalex-snapshot
Correction of the NMR structure of the ETS1/DNA complex
inferredcites →https://doi.org/10.1038/emboj.2010.106openalex-snapshot
Genome‐wide analysis of ETS‐family DNA‐binding in vitro and in vivo
inferredcites →https://doi.org/10.1038/nbt.2136openalex-snapshot
Massively parallel functional dissection of mammalian enhancers in vivo
inferredcites →https://doi.org/10.1038/nbt.2137openalex-snapshot
Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay
inferredcites →https://doi.org/10.1038/ng.2713openalex-snapshot
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model
inferredcites →https://doi.org/10.1073/pnas.1210678109openalex-snapshot
Complex effects of nucleotide variants in a mammalian cis -regulatory element
inferredcites →https://doi.org/10.1073/pnas.1307449110openalex-snapshot
Massively parallel in vivo enhancer assay reveals that highly local features determine the cis -regulatory function of ChIP-seq peaks
inferredcites →https://doi.org/10.1074/jbc.270.41.24532openalex-snapshot
Identification of Essential GATA and Ets Binding Motifs within the Promoter of the Platelet Glycoprotein Ibα Gene
inferredcites →https://doi.org/10.1093/nar/29.12.2471openalex-snapshot
Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay
inferredcites →https://doi.org/10.1093/nar/gkt1282openalex-snapshot
The 2014Nucleic Acids ResearchDatabase Issue and an updated NAR online Molecular Biology Database Collection
inferredcites →https://doi.org/10.1093/nar/gkt437openalex-snapshot
DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale
inferredcites →https://doi.org/10.1101/gad.6.6.965openalex-snapshot
A novel modulator domain of Ets transcription factors.
inferredcites →https://doi.org/10.1101/gr.093047.109openalex-snapshot
Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery
inferredcites →https://doi.org/10.1101/gr.169243.113openalex-snapshot
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
inferredcites →https://doi.org/10.1101/gr.184671.114openalex-snapshot
A widespread role of the motif environment in transcription factor binding across diverse protein families
inferredcites →https://doi.org/10.1101/gr.185033.114openalex-snapshot
Unraveling determinants of transcription factor binding outside the core binding site
inferredcites →https://doi.org/10.1126/science.1080049openalex-snapshot
The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins
inferredcites →https://doi.org/10.1126/science.1145893openalex-snapshot
Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression
inferredcites →https://doi.org/10.1126/science.1169050openalex-snapshot
Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome
inferredcites →https://doi.org/10.1126/science.1229223openalex-snapshot
Probing Allostery Through DNA
inferredcites →https://doi.org/10.1126/science.aac6948openalex-snapshot
Suboptimization of developmental enhancers
inferredcites →https://doi.org/10.1128/mcb.13.7.3999openalex-snapshot
DNA-Binding Specificity of GATA Family Transcription Factors
inferredcites →https://doi.org/10.1146/annurev-biochem-060408-091030openalex-snapshot
Origins of Specificity in Protein-DNA Recognition
inferredcites →https://doi.org/10.1186/s12859-015-0819-2openalex-snapshot
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system
inferredcites →https://doi.org/10.1242/dev.00200openalex-snapshot
A conserved role for the MEK signalling pathway in neural tissue specification and posteriorisation in the invertebrate chordate, the ascidianCiona intestinalis
inferredcites →https://doi.org/10.1242/dev.010850openalex-snapshot
A combinatorial code of maternal GATA, Ets and β-catenin-TCF transcription factors specifies and patterns the early ascidian ectoderm
inferredcites →https://doi.org/10.1242/dev.036160openalex-snapshot
Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila
inferredcites →https://doi.org/10.1242/dev.124.10.1851openalex-snapshot
The hardwiring of development: organization and function of genomic regulatory systems
inferredcites →https://doi.org/10.1371/journal.pbio.1000343openalex-snapshot
Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species
inferredcites →https://doi.org/10.1371/journal.pgen.1002053openalex-snapshot
Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules
inferredcites →https://doi.org/10.1371/journal.pgen.1002095openalex-snapshot
Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element
inferredcites →https://doi.org/10.1371/journal.pone.0000916openalex-snapshot
A Multicassette Gateway Vector Set for High Throughput and Comparative Analyses in Ciona and Vertebrate Embryos
inferredcites →https://doi.org/10.4161/trns.28848openalex-snapshot
Variation in Vertebrate Cis-Regulatory Elements in Evolution and Disease
inferredcites →https://doi.org/10.7554/elife.04837openalex-snapshot
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41467-025-66861-yopenalex-snapshot
Discovering the complete enhancer map of human herpesviruses using a natural language processing model
inferred← citeshttps://doi.org/10.1101/138701openalex-snapshot
An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time
inferred← citeshttps://doi.org/10.21203/rs.3.rs-6313466/v1openalex-snapshot
Repressive Roles of Erf and Elk in FGF-Regulated Neural Development in Ciona intestinalis
inferred← citeshttps://doi.org/10.7554/elife.29656openalex-snapshot
An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time
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