Source 1primary paper2016PLoS ONE
Toolkit/quantitative chromatin immunoprecipitation
quantitative chromatin immunoprecipitation
Also known as: qChIP
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Quantitative chromatin immunoprecipitation (qChIP) is an assay method for measuring protein association with specific chromatin regions. In the cited Ustilago maydis study, qChIP analysis supported direct binding of the UPR regulator Cib1 to UPRE-containing promoter fragments of pit2 and tin1-1.
Usefulness & Problems
Why this is useful
qChIP is useful for testing whether a specific DNA-binding protein is associated with defined genomic loci in chromatin. In the cited work, it provided locus-specific evidence linking Cib1 occupancy to promoters of genes encoding secreted virulence factors.
Problem solved
This assay addresses the problem of determining whether a candidate regulator directly binds particular promoter regions rather than affecting target gene expression only indirectly. In the cited example, it was used to assess direct association of Cib1 with UPRE-containing promoter fragments.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Mechanisms
chromatin immunoprecipitationchromatin immunoprecipitationquantitative locus-specific detection of protein-dna bindingquantitative locus-specific detection of protein-dna bindingTechniques
Functional AssayTarget processes
No target processes tagged yet.
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: sensor
The available evidence indicates use of quantitative chromatin immunoprecipitation analysis in Ustilago maydis to examine Cib1 association with UPRE-containing promoter fragments of pit2 and tin1-1. The supplied material does not specify antibody strategy, crosslinking conditions, detection chemistry, normalization approach, or construct design.
The supplied evidence is limited to a single statement that qChIP analysis was performed and supported Cib1 binding at two promoters. No methodological details, performance metrics, controls, resolution limits, or broader validation across additional loci are provided in the supplied evidence.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Approval Evidence
1 source1 linked approval claimfirst-pass slug quantitative-chromatin-immunoprecipitation
quantitative chromatin immunoprecipitation (qChIP) analysis
Source:
binding interactionsupports
Cib1 directly binds UPRE-containing promoter fragments of pit2 and tin1-1.
direct binding of the Hac1-homolog Cib1 to the UPRE containing promoter fragments of both genes was confirmed by quantitative chromatin immunoprecipitation (qChIP) analysis
Source:
Comparisons
Source-backed strengths
The evidence supports that qChIP can provide quantitative, locus-specific detection of protein-DNA association in chromatin. In Ustilago maydis, it supported direct binding of Cib1 at the pit2 and tin1-1 promoters, connecting promoter occupancy to a defined cis-element context.
Compared with chromatin immunoprecipitation sequencing
quantitative chromatin immunoprecipitation and chromatin immunoprecipitation sequencing address a similar problem space.
Shared frame: same top-level item type; shared mechanisms: chromatin immunoprecipitation
Compared with Field-domain rapid-scan EPR at 240 GHz
quantitative chromatin immunoprecipitation and Field-domain rapid-scan EPR at 240 GHz address a similar problem space.
Shared frame: same top-level item type
Compared with native green gel system
quantitative chromatin immunoprecipitation and native green gel system address a similar problem space.
Shared frame: same top-level item type
Strengths here: looks easier to implement in practice.
Ranked Citations
- 1.