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).

• 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

• Nanog mediated control of TBX3-GATA6 circuitry in primitive endoderm differentiation of mESCs.

  PMID 41629627 · PMC12979688 · EMBO reports · 2026 · 8 claims · 8 setups

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  NANOG partners with TBX3 and the PRC2 complex to maintain ESC identity by silencing PrE genes through distal enhancers

  rcnβh escs qpcr rna-seq chip-seq

• HIF sustain a transcriptional regulatory circuit of EPAS1 expression in renal clear cell carcinoma.

  PMID 41714613 · PMC12921326 · Nature communications · 2026 · 8 claims · 8 setups

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  HIF-2α mRNA is specifically overexpressed in ccRCC tumor tissue/cells compared to normal kidney, while it is reduced in papillary and chromophobe RCC

  erlangen tcga ccrcc tubule qpcr rna-seq rnascope

• An epigenomic investigation of atrial fibrillation in a matched left and right atrial human cohort.

  PMID 41906156 · PMC13045105 · Clinical epigenetics · 2026 · 8 claims · 6 setups

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  H3K27ac epigenomic profiles differ more strongly by anatomical side (left vs right atrium) than by disease status (AF vs SR)

  left independent paired ipsc-derived h3k27ac bulk rt-qpcr

• PVT1 lincRNA signals an androgen-dependent transcriptional activation program of oncogenes in prostate cancer cells.

  PMID 41792045 · PMC13139993 · International journal of cancer · 2026 · 8 claims · 7 setups

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  PVT1 knockdown significantly reduces LNCaP cell proliferation and increases sensitivity to apoptosis

  lncap tcga-prad rt-qpcr trypan transwell

• Cis-Regulation of the CFTR Gene in Pancreatic Cells.

  PMID 40332394 · PMC12027686 · International journal of molecular sciences · 2025 · 7 claims · 8 setups

  Has reproduction · 50

  Multiple active CREs exist upstream and downstream of the CFTR gene in pancreatic (Capan-1) cells, identified via ATAC-seq, CUT&RUN-seq (H3K27ac), 4C-seq, and the ABC model

  capan-1 caco-2 hepg2 atac-seq cut&run-seq 4c-seq

• Predicting the effect of CRISPR-Cas9-based epigenome editing.

  PMID 41524535 · PMC12795505 · eLife · 2026 · 8 claims · 6 setups

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  Machine learning (CNN and ridge regression) models trained on histone PTM ChIP-seq and RNA-seq data from 13 ENCODE cell types accurately predict endogenous gene expression, with transcriptome-wide correlations of ~0.70-0.79 for most cell types

  hek293t k562 computational chip-seq rna-seq mnase-seq

• Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites.

  PMID 41778583 · PMC12959880 · eLife · 2026 · 8 claims · 8 setups

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  H3K115ac is enriched at the TSS of active CpG island (CGI) promoters, far more than non-CGI promoters

  embryonic mescs synthetic mesc chip-seq atac-seq dot

• β-Catenin activity induces an RNA biosynthesis program promoting therapy resistance in T-cell acute lymphoblastic leukemia.

  PMID 36597789 · PMC9906382 · EMBO molecular medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 65

  β-catenin binds directly to promoters of RNA processing, splicing, and ribosomal biogenesis genes in T-ALL cells

  rpmi8402 chipseq chip-qpcr sequencing

• EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology.

  PMID 41805684 · PMC12975130 · eLife · 2026 · 8 claims · 8 setups

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  EPB41L4A-AS1 acts in cis to enhance transcription of the proximal EPB41L4A gene

  mcf-7 epb41l4a-as1 rna-seq rt-qpcr single-molecule

• Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

  PMID 40216980 · PMC12117045 · EMBO reports · 2025 · 8 claims · 11 setups

  Has reproduction · 90

  MYC eRNAs (notably MYC-490-kb) are transcribed from the MYC super-enhancer and are upregulated by chronic TNF-α stimulation specifically in pancreatic cancer cells, not normal pancreatic epithelial cells

  pdac miapaca-2 chronic myc-490-kb survival chip-seq nascent

• YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPARγ and its target enhancers.

  PMID 41533786 · PMC12802833 · Science advances · 2026 · 8 claims · 8 setups

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  TAZ represses PPARγ-bound target enhancers, evidenced by markedly reduced H3K27ac occupancy, leading to transcriptional repression of adipogenic genes including Pparg2

  c3h10t1 inguinal iwat adipose atac-seq rna-seq immunoblot

• Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.

  PMID 41857393 · PMC13061643 · Nature neuroscience · 2026 · 8 claims · 6 setups

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  Adult spinal-cord-derived human oligodendroglia and astrocytes, but not microglia, show primed chromatin signatures at HOX loci and a putative SOX10 enhancer.

  postmortem induced lentiviral cns single-nucleus nanocut&tag high-resolution

• Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.

  PMID 35710138 · PMC9296009 · Genes & development · 2022 · 8 claims · 7 setups

  Has reproduction · 81

  Sox2 transcriptional activation is traced almost entirely to two key transcription factor-bound regions (SRR107 and SRR111) within the SCR

  escs esc sequence compiled allele-specific chip-seq motif

• TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.

  PMID 23233547 · PMC3589534 · Genome research · 2013 · 8 claims · 8 setups

  Has reproduction · 78

  TRIM28 repression of ERVs protects cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements.

  embryonic trim28 mrna-seq trim28 h3k9me3

• CITED2 is a druggable epigenetic switch coupling neuronal maturation to regenerative decline.

  PMID 41731079 · PMC13083982 · EMBO molecular medicine · 2026 · 8 claims · 8 setups

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  The transition from immature non-polarized to mature polarized DRG neurons (E12.5-E17.5) is associated with loss of gene expression signatures needed for regenerative growth competence.

  drg sciatic rna-seq integrated immunofluorescence

• A conserved hormonal signalling-H2A.Z axis rapidly reorganizes 3D chromatin interactions in adipocyte thermogenesis.

  PMID 42014869 · PMC13218939 · Nature metabolism · 2026 · 8 claims · 8 setups

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  β3-AR signalling rapidly reorganizes chromatin loops within 4 hours of stimulation

  brown rna-seq micro-c pro-seq

• Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.

  PMID 33086062 · PMC7649750 · Cell reports · 2020 · 8 claims · 8 setups

  Has reproduction · 59

  KMT2D is a potent tumor suppressor in melanoma

  hmel-brafv600e tyr-creert2 tma kmt2d pooled xenograft genetically

• Gene Regulatory Interactions at Lamina-Associated Domains.

  PMID 36833261 · PMC9957430 · Genes · 2023 · 8 claims · 8 setups

  Has reproduction · 31

  Active genes in constitutive LADs (cLADs) reside in euchromatic regions with low LMNB1 and LMNA/C enrichment, i.e., are locally detached from the nuclear lamina

  adipose ascs mesenchymal chip-seq rna-seq atac-seq

• Cohesin regulates alternative splicing.

  PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups

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  Cohesin regulates alternative splicing independently of its effects on transcription.

  hct116rmac hct116 recombinant hek293 bulk rt-pcr proximity