ChIP-qPCR

Overview

Chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR) measures the occupancy of a specific protein (transcription factor, histone mark, or chromatin modifier) at a defined genomic locus. Chromatin is crosslinked, sheared, and immunoprecipitated with the target antibody; the enrichment of a specific promoter or enhancer region in the pulldown is then quantified by qPCR relative to input chromatin.

Used by

  • ChIP-qPCR used to confirm TEAD1 binding at the SEMA7A promoter in gallbladder fibroblasts, with enrichment under stiff (16 kPa) vs soft (0.5 kPa) matrix conditions; separately, rh-SEMA7A increased p300 (EP300) occupancy and H3K27ac at the SNAI1 and ZEB1 promoters in GBC cells, and the p300 S1834A phosphodead mutant abolished H3K27ac enrichment PMID:24997986
  • Used to confirm EWS::FLI1 ChIP-seq binding peaks in BRCA1 exons 11 and 15 in EWS::FLI1-transduced heMSCs; siRNA abolition of binding validated specificity. PMID:25186949
  • Used for H3K27me3 and H3K4me3 chromatin-immunoprecipitation in MPNST cell lines to validate that SUZ12 re-expression restored repressive marks at FOXN4, IGF2, PAX2, TLX1 promoters PMID:25240281
  • Used alongside ChIP-seq to validate DUX4 occupancy at ERG exon 6 alt and other loci in NALM-6 and Reh cell lines in the DUX4/ERG B-ALL study. PMID:27776115
  • Used ChIP-qPCR to validate chromatin immunoprecipitation enrichment at target loci PMID:28196596
  • ChIP-qPCR and allele-specific ChIP-AS-qPCR confirmed preferential USF1 and H3K4me1/H3K27ac enrichment at the rs4519489 A allele in heterozygous prostate cancer tissues; USF1 ChIP-seq in heterozygous tissue showed A:T ratio shift from 1:5 (input) to 11:6 (USF1-IP) PMID:28927585

Notes

  • ChIP-qPCR is a targeted approach suitable for validating specific loci; ChIP-seq provides genome-wide occupancy maps.
  • H3K27ac is a mark of active enhancers and promoters; its detection at target loci serves as a functional readout of transcriptional activation.
  • Results are typically expressed as percent input or enrichment over IgG control.

Sources

This page was processed by entity-page-writer on 2026-05-11. - PMID:25186949

This page was processed by entity-page-writer on 2026-05-11. - PMID:25240281

This page was processed by entity-page-writer on 2026-05-11. - PMID:27776115

This page was processed by entity-page-writer on 2026-05-15. - PMID:28196596

This page was processed by wiki-cli on 2026-05-14. - PMID:28927585

This page was processed by wiki-cli on 2026-05-15.