Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern.

  PMID 19908860 · PMC2787777 · Journal of the American Chemical Society · 2009 · 8 claims · 6 setups

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  The full-length bcl-2 C-rich promoter sequence (Py39WT) forms one major intramolecular i-motif structure with a transitional pH of 6.6

  py39wt fam 32p-labeled circular melting fret

• Temporal constraints on enhancer usage shape the regulation of limb gene transcription.

  PMID 41526337 · PMC12795824 · Nature communications · 2026 · 8 claims · 6 setups

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  Putative enhancer repertoires at limb developmental gene loci shift over time, with distinct early-acting, common-acting, and late-acting enhancers.

  limb shox2 h3k27ac transgenic bulk

• Isoform-specific single-cell perturb-seq reveals distinct functions of alternative promoters in drug response.

  PMID 41728950 · PMC12926921 · Nucleic acids research · 2026 · 5 claims · 8 setups

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  CRISPR-dCas9-based screens exhibit widespread promoter specificity, with untargeted promoters often showing compensatory upregulation to maintain overall gene expression

  mcf-7 rpe1 mcf-7-dcas9 tissue-wide isoform-specific reanalysis qrt-pcr

• EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.

  PMID 41832145 · PMC13133354 · Nature communications · 2026 · 8 claims · 7 setups

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  EPInformer outperforms existing gene expression prediction models (Xpresso, CREaTor, Seq-GraphReg, Enformer, Borzoi) in rigorous 12-fold cross-chromosome validation for both RNA-seq and CAGE expression prediction

  k562 lines likely cell-type-specific rna-seq cage abc

• The changing face of genomics.

  PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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  Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

  yeast drosophila zebrafish elegans chip-chip comparative insertional

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Transcriptional bursting kinetics is regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 (PRC2) and transcription elongation factors

  cast knock-in mesc mescs single-cell single-molecule flow

• A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.

  PMID 37277355 · PMC10241789 · Nature communications · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  2232 genome-wide putative super-enhancers (SEs) were identified in mouse cranial neural crest cell (CNCC) subpopulations

  e10.5 embryonic pa2 h3k27ac promoter hi-c

• Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

  PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups

  Has reproduction · 93

  An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.

  hff mrc5 chip-qpcr rt-qpcr chipseq

• A 14-bp motif in the KIT active promoter region is critical for melanin accumulation in yaks, mice, and humans.

  PMID 40629379 · PMC12239316 · BMC biology · 2025 · 8 claims · 7 setups

  Has reproduction · 54

  A 14-bp deletion in the KIT gene promoter region is associated with the all-white phenotype in yaks, identified via GWAS

  domestic re-sampled hek293t yak whole-genome pcr dual-luciferase

• Tissue plasminogen activator and plasminogen activator inhibitor type 1 gene polymorphism in patients with gastric ulcer complicated with bleeding.

  PMID 12589088 · PMC3054991 · Journal of Korean medical science · 2003 · 6 claims · 5 setups

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  The t-PA I/D or D/D genotype is significantly associated with duodenal (vs gastric) ulcer location

  genomic randomly patients endoscopic allele-specific pcr logistic

• TP73 allelic expression in human brain and allele frequencies in Alzheimer's disease.

  PMID 15175114 · PMC420466 · BMC medical genetics · 2004 · 8 claims · 6 setups

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  A -386G/A SNP in the TP73 P3 promoter is weakly but significantly associated with AD risk in a tri-ethnic elderly population.

  brain peripheral sk-nsh-n genomic rt-pcr direct snp

• Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

  PMID 16542438 · PMC1526716 · BMC medical genetics · 2006 · 8 claims · 6 setups

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  Mutations in the OAZ3 gene are not a common cause of male infertility

  genomic coding inferred oaz3 direct sscp haplotype

• Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

  PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

  hela hs578t nih3t3 genomic chap-chip conventional scanning

• Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

  PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

  pediatric tumor eight desmoplastic aprimes bisulfite quantitative

• Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

  PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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  A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

  myeloid reference selected genome-localized microarray promoter k-medoids

• Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia.

  PMID 19835597 · PMC2770485 · Molecular cancer · 2009 · 8 claims · 8 setups

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  MLL-mutant (MLL mu) AML cell lines show significantly lower TSG promoter methylation than MLL wild-type (MLL wt) AML cell lines

  acute mll lines bone ms-mlpa hhai methylation-specific

• Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

  PMID 19747392 · PMC2754481 · BMC evolutionary biology · 2009 · 8 claims · 5 setups

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  The coding sequence of FGF5 is not the critical determinant of hair length differences among elephantids, including the woolly mammoth.

  asian fgf5 woolly savanna pcr structural blast

• Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes.

  PMID 41501500 · PMC12881478 · Communications biology · 2026 · 8 claims · 8 setups

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  The white adipocyte transcriptional program is tightly linked to promoter-level modulation of H3K27ac and chromatin accessibility.

  adipose asc-derived white ascs bulk atac-seq chip-seq

• Architectural and evolutionary features of TE-derived TSSs shape tissue-specific promoter activity in the human genome.

  PMID 41620470 · PMC12963367 · Nature communications · 2026 · 8 claims · 8 setups

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  A three-step RAMPAGE-based pipeline can systematically identify TE-derived transcription start sites (TSSs) genome-wide, distinguishing them from autonomous TE transcription and background noise.

  biosamples same k562 genomic rampage rna-seq h3k4me3

• A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters.

  PMID 30332484 · PMC6192621 · PloS one · 2018 · 8 claims · 8 setups

  Has reproduction · 63

  The CGCG element (consensus TCTCGCGAGA) is a novel promoter motif enriched in TATA-less CpG island-associated promoters of ribosomal protein and housekeeping genes

  k562 hek293t hek293t-derived motif gro-cap luciferase