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Nucleotide composition-linked divergence of vertebrate core promoter architecture
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/j.1538-7305.1948.tb01338.xopenalex-snapshot
A Mathematical Theory of Communication
inferredcites →https://doi.org/10.1016/0022-2836(87)90689-9openalex-snapshot
CpG Islands in vertebrate genomes
inferredcites →https://doi.org/10.1016/0092-8674(89)90176-1openalex-snapshot
The “initiator” as a transcription control element
inferredcites →https://doi.org/10.1016/j.biocel.2007.09.004openalex-snapshot
A short ultraconserved sequence drives transcription from an alternate FBN1 promoter
inferredcites →https://doi.org/10.1016/j.ceb.2008.03.003openalex-snapshot
The RNA polymerase II core promoter — the gateway to transcription
inferredcites →https://doi.org/10.1016/j.devcel.2009.08.005openalex-snapshot
A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos
inferredcites →https://doi.org/10.1016/j.gene.2003.09.028openalex-snapshot
Ets ternary complex transcription factors
inferredcites →https://doi.org/10.1016/j.jmb.2004.02.048openalex-snapshot
Constrained Binding Site Diversity within Families of Transcription Factors Enhances Pattern Discovery Bioinformatics
inferredcites →https://doi.org/10.1016/j.ydbio.2009.08.009openalex-snapshot
Regulation of gene expression via the core promoter and the basal transcriptional machinery
inferredcites →https://doi.org/10.1016/s0167-4781(02)00343-3openalex-snapshot
Nuclear activators and coactivators in mammalian mitochondrial biogenesis
inferredcites →https://doi.org/10.1038/290310a0openalex-snapshot
The SV40 early region TATA box is required for accurate in vitro initiation of transcription
inferredcites →https://doi.org/10.1038/371435a0openalex-snapshot
Spl elements protect a CpG island from de novo methylation
inferredcites →https://doi.org/10.1038/emm.2002.36openalex-snapshot
The DPE, a core promoter element for transcription by RNA polymerase II
inferredcites →https://doi.org/10.1038/nature03441openalex-snapshot
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
inferredcites →https://doi.org/10.1038/nature08924openalex-snapshot
CpG islands influence chromatin structure via the CpG-binding protein Cfp1
inferredcites →https://doi.org/10.1038/nbt1053openalex-snapshot
Assessing computational tools for the discovery of transcription factor binding sites
inferredcites →https://doi.org/10.1038/nbt1206-1471openalex-snapshot
NCBI GEO standards and services for microarray data
inferredcites →https://doi.org/10.1038/nbt717openalex-snapshot
An algorithm for finding protein–DNA binding sites with applications to chromatin- immunoprecipitation microarray experiments
inferredcites →https://doi.org/10.1038/ng.375openalex-snapshot
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
inferredcites →https://doi.org/10.1038/ng1789openalex-snapshot
Genome-wide analysis of mammalian promoter architecture and evolution
inferredcites →https://doi.org/10.1038/nrg2026openalex-snapshot
Mammalian RNA polymerase II core promoters: insights from genome-wide studies
inferredcites →https://doi.org/10.1038/sj.emboj.7601550openalex-snapshot
Identification of novel functional TBP‐binding sites and general factor repertoires
inferredcites →https://doi.org/10.1042/bst0341047openalex-snapshot
Perspectives on the RNA polymerase II core promoter
inferredcites →https://doi.org/10.1042/bst0341051openalex-snapshot
Core promoter elements recognized by transcription factor IIB
inferredcites →https://doi.org/10.1073/pnas.0405536101openalex-snapshot
Specialized and redundant roles of TBP and a vertebrate-specific TBP paralog in embryonic gene regulation in Xenopus
inferredcites →https://doi.org/10.1073/pnas.77.12.7024openalex-snapshot
Specific in vitro transcription of conalbumin gene is drastically decreased by single-point mutation in T-A-T-A box homology sequence.
inferredcites →https://doi.org/10.1073/pnas.91.1.192openalex-snapshot
A glutamine-rich hydrophobic patch in transcription factor Sp1 contacts the dTAFII110 component of the Drosophila TFIID complex and mediates transcriptional activation.
inferredcites →https://doi.org/10.1074/jbc.m403818200openalex-snapshot
Cbf1p Is Required for Chromatin Remodeling at Promoter-proximal CACGTG Motifs in Yeast
inferredcites →https://doi.org/10.1093/bioinformatics/17.12.1113openalex-snapshot
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
inferredcites →https://doi.org/10.1093/bioinformatics/btn420openalex-snapshot
MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders
inferredcites →https://doi.org/10.1093/dnares/dsq016openalex-snapshot
Comprehensive Analysis of the Palindromic Motif TCTCGCGAGA: A Regulatory Element of the HNRNPK Promoter
inferredcites →https://doi.org/10.1093/nar/18.20.6097openalex-snapshot
Sequence logos: a new way to display consensus sequences
inferredcites →https://doi.org/10.1093/nar/gkh465openalex-snapshot
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
inferredcites →https://doi.org/10.1093/nar/gki791openalex-snapshot
Limitations and potentials of current motif discovery algorithms
inferredcites →https://doi.org/10.1093/nar/gkm201openalex-snapshot
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
inferredcites →https://doi.org/10.1093/nar/gkm310openalex-snapshot
SCOPE: a web server for practical de novo motif discovery
inferredcites →https://doi.org/10.1093/nar/gkn137openalex-snapshot
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
inferredcites →https://doi.org/10.1093/nar/gkp066openalex-snapshot
Massive transcriptional start site analysis of human genes in hypoxia cells
inferredcites →https://doi.org/10.1093/nar/gkp335openalex-snapshot
MEME SUITE: tools for motif discovery and searching
inferredcites →https://doi.org/10.1093/nar/gkp423openalex-snapshot
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships
inferredcites →https://doi.org/10.1101/gad.10.6.711openalex-snapshot
Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters.
inferredcites →https://doi.org/10.1101/gad.1193404openalex-snapshot
The MTE, a new core promoter element for transcription by RNA polymerase II
inferredcites →https://doi.org/10.1101/gad.12.1.34openalex-snapshot
New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB
inferredcites →https://doi.org/10.1101/gad.342405openalex-snapshot
A core promoter element downstream of the TATA box that is recognized by TFIIB
inferredcites →https://doi.org/10.1101/gad.8.19.2282openalex-snapshot
Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island.
inferredcites →https://doi.org/10.1101/gad.8.7.821openalex-snapshot
Direct recognition of initiator elements by a component of the transcription factor IID complex.
inferredcites →https://doi.org/10.1101/gr.112128.110openalex-snapshot
Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
inferredcites →https://doi.org/10.1101/gr.1953904openalex-snapshot
Clustering of DNA Sequences in Human Promoters
inferredcites →https://doi.org/10.1101/gr.5754707openalex-snapshot
Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1
inferredcites →https://doi.org/10.1101/gr.6831208openalex-snapshot
A code for transcription initiation in mammalian genomes
inferredcites →https://doi.org/10.1101/gr.849004openalex-snapshot
WebLogo: A Sequence Logo Generator: Figure 1
inferredcites →https://doi.org/10.1111/j.1440-169x.2005.00797.xopenalex-snapshot
Sp1‐like transcription factors are regulators of embryonic development in vertebrates
inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1126/science.1183670openalex-snapshot
The Genome of the Western Clawed Frog Xenopus tropicalis
inferredcites →https://doi.org/10.1126/science.7824954openalex-snapshot
Cloning of an Intrinsic Human TFIID Subunit That Interacts with Multiple Transcriptional Activators
inferredcites →https://doi.org/10.1128/mcb.01363-06openalex-snapshot
The New Core Promoter Element XCPE1 (X Core Promoter Element 1) Directs Activator-, Mediator-, and TATA-Binding Protein-Dependent but TFIID-Independent RNA Polymerase II Transcription from TATA-Less Promoters
inferredcites →https://doi.org/10.1128/mcb.01462-06openalex-snapshot
hDREF Regulates Cell Proliferation and Expression of Ribosomal Protein Genes
inferredcites →https://doi.org/10.1128/mcb.14.3.1582openalex-snapshot
Species-specific interaction of the glutamine-rich activation domains of Sp1 with the TATA box-binding protein.
inferredcites →https://doi.org/10.1128/mcb.21.4.1001-1010.2001openalex-snapshot
Recruitment of an RNA Polymerase II Complex Is Mediated by the Constitutive Activation Domain in CREB, Independently of CREB Phosphorylation
inferredcites →https://doi.org/10.1146/annurev.biochem.72.121801.161520openalex-snapshot
The RNA Polymerase II Core Promoter
inferredcites →https://doi.org/10.1186/1471-2105-8-s6-s3openalex-snapshot
Computational analyses of eukaryotic promoters
inferredcites →https://doi.org/10.1186/1471-2105-8-s7-s21openalex-snapshot
A survey of DNA motif finding algorithms
inferredcites →https://doi.org/10.1186/1471-2164-10-146openalex-snapshot
The evolution of isochore patterns in vertebrate genomes
inferredcites →https://doi.org/10.1186/1471-2164-7-161openalex-snapshot
The features of Drosophila core promoters revealed by statistical analysis
inferredcites →https://doi.org/10.1186/gb-2002-3-12-research0087openalex-snapshot
Computational analysis of core promoters in the Drosophila genome
inferredcites →https://doi.org/10.1186/gb-2006-7-7-r53openalex-snapshot
Comparative genomics of Drosophila and human core promoters
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1371/journal.pcbi.0030061openalex-snapshot
DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
inferredcites →https://doi.org/10.1371/journal.pone.0005103openalex-snapshot
Characterization of Transcription from TATA-Less Promoters: Identification of a New Core Promoter Element XCPE2 and Analysis of Factor Requirements
inferredcites →https://doi.org/10.18388/abp.2007_3273openalex-snapshot
A common cis-element in promoters of protein synthesis and cell cycle genes.
inferredcites →https://doi.org/10.4135/9781412959384.n229openalex-snapshot
Mathematical Theory of Communication
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.2139/ssrn.4755772openalex-extracted
Cross-Validation of Conserved Osteoblast-Specific Enhancers Illuminates Bone Diseases and Early Skeletal Evolution
inferred← citeshttps://doi.org/10.1002/9781118492833.ch20openalex-snapshot
Genomics and Genome Engineering in Xenopus
inferred← citeshttps://doi.org/10.1002/dvg.20831openalex-snapshot
The epigenome in early vertebrate development
inferred← citeshttps://doi.org/10.1007/978-1-61779-992-1_17openalex-snapshot
Chromatin Immunoprecipitation Analysis of Xenopus Embryos
inferred← citeshttps://doi.org/10.1016/bs.adgen.2016.05.001openalex-snapshot
Transcriptional Regulation During Zygotic Genome Activation in Zebrafish and Other Anamniote Embryos
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Establishing pluripotency in early development
inferred← citeshttps://doi.org/10.1016/j.bpj.2017.04.023openalex-snapshot
Specificity-Determining DNA Triplet Code for Positioning of Human Preinitiation Complex
inferred← citeshttps://doi.org/10.1016/j.cdev.2024.203924openalex-snapshot
Xenopus tropicalis osteoblast-specific open chromatin regions reveal promoters and enhancers involved in human skeletal phenotypes and shed light on early vertebrate evolution
inferred← citeshttps://doi.org/10.1016/j.tig.2011.08.001openalex-snapshot
Genomic and chromatin signals underlying transcription start-site selection
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02216openalex-snapshot
Prompt-CBP: A Novel Prompt Learning-Based Model for Predicting Cross-Species Promoters
inferred← citeshttps://doi.org/10.1038/nrg3163openalex-snapshot
Metazoan promoters: emerging characteristics and insights into transcriptional regulation
inferred← citeshttps://doi.org/10.1038/srep22496openalex-snapshot
Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome
inferred← citeshttps://doi.org/10.1101/2023.08.30.555543openalex-snapshot
Architecture and evolutionary conservation of Xenopus tropicalis osteoblast-specific regulatory regions shed light on bone diseases and early skeletal evolution
inferred← citeshttps://doi.org/10.1101/gr.114843.110openalex-snapshot
Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
inferred← citeshttps://doi.org/10.1101/gr.153692.112openalex-snapshot
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
inferred← citeshttps://doi.org/10.1101/gr.159608.113openalex-snapshot
Principles of nucleation of H3K27 methylation during embryonic development
inferred← citeshttps://doi.org/10.1101/gr.184648.114openalex-snapshot
Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
inferred← citeshttps://doi.org/10.1101/pdb.top097915openalex-snapshot
Genomics Methods for Xenopus Embryos and Tissues
inferred← citeshttps://doi.org/10.1186/1756-0500-4-300openalex-snapshot
Affinity-based enrichment strategies to assay methyl-CpG binding activity and DNA methylation in early Xenopus embryos
inferred← citeshttps://doi.org/10.1186/s12915-015-0116-6openalex-snapshot
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles
inferred← citeshttps://doi.org/10.1186/s12977-015-0161-9openalex-snapshot
Human endogenous retroviruses sustain complex and cooperative regulation of gene-containing loci and unannotated megabase-sized regions
inferred← citeshttps://doi.org/10.1201/9781003050230-13openalex-snapshot
Dynamics of Chromatin Remodeling during Embryonic Development
inferred← citeshttps://doi.org/10.1266/ggs.22-00137openalex-snapshot
Promoter generation for the chimeric sex-determining gene dm-W in Xenopus frogs
inferred← citeshttps://doi.org/10.1371/journal.pgen.1003906openalex-snapshot
Decoding a Signature-Based Model of Transcription Cofactor Recruitment Dictated by Cardinal Cis-Regulatory Elements in Proximal Promoter Regions
inferred← citeshttps://doi.org/10.1371/journal.pgen.1006538openalex-snapshot
Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression
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Combined Chromatin and Expression Analysis Reveals Specific Regulatory Mechanisms within Cytokine Genes in the Macrophage Early Immune Response
inferred← citeshttps://doi.org/10.1371/journal.pone.0187243openalex-snapshot
Nucleotide patterns aiding in prediction of eukaryotic promoters
inferred← citeshttps://doi.org/10.15252/embj.201695323openalex-snapshot
GT‐rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes
inferred← citeshttps://doi.org/10.1534/g3.113.008680openalex-snapshot
Large-Scale Quality Analysis of Published ChIP-seq Data
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The Dynamics of Histone Modifications during Mammalian Zygotic Genome Activation
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