DECK 2: Enhancer Identification Methods (Matching Mode)

connect each experimental method with what it specifically measures and what it reveals about enhancers. Essay questions often ask "How are enhancers identified?" - this deck gives you the complete answer

methods

DNase-seq Method What it Measures What it Reveals About Enhancers    ATAC-seq DNase-seq Chromatin accessibility (open regions) Identifies potential regulatory regions (promoters, enhancers)
   MNase-seq ATAC-seq Chromatin accessibility (open regions) Identifies nucleosome-free regions; uses TN5 transposase
   FAIRE-seq MNase-seq Nucleosome positioning Reveals nucleosome depletion at active regulatory elements
   ChIP-seq (H3K27ac) FAIRE-seq Open chromatin (formaldehyde-assisted isolation) Identifies regulatory elements without crosslinking    ChIP-seq (H3K4me1) ChIP-seq (H3K27ac) Histone modification Marks active enhancers
   ChIP-seq (H3K27me3) ChIP-seq (H3K4me1) Histone modification Marks primed/active enhancers
   ChIP-seq (P300) ChIP-seq (H3K27me3) Histone modification Marks poised/repressed enhancers (Polycomb)    3C ChIP-seq (P300) Transcription co-activator binding Identifies active enhancer regions
   4C 3C One-to-one interactions Confirms known enhancer-promoter loops
   Hi-C 4C One-to-many interactions Identifies all regions interacting with a locus of interest    Capture-C Hi-C All-to-all interactions Genome-wide interaction maps (low resolution)
   Micro-C Capture-C Many-to-all interactions High-resolution mapping of specific region interactions    ChIA-PET Micro-C All-to-all (highest resolution) Genome-wide enhancer-promoter loops at nucleosome resolution
   HiChIP ChIA-PET Many-to-many (with antibody) Identifies loops mediated by specific proteins
   LacZ reporter HiChIP Many-to-many (with antibody) Enriches for loops involving specific histone marks/TFs    CAT reporter LacZ reporter Functional validation Tests if a DNA region drives tissue-specific expression

DNase-seq What it Measures CAT reporter Functional validation Measures transcriptional activity of regulatory elements

ATAC-seq What it Measures

Chromatin accessibility (open regions)

MNase-seq What it Measures

Chromatin accessibility (open regions)

FAIRE-seq What it Measures

Nucleosome positioning

ChIP-seq (H3K27ac) What it Measures

Open chromatin (formaldehyde-assisted isolation)

ChIP-seq (H3K4me1) What it Measures

Histone modification

ChIP-seq (H3K27me3) What it Measures

Histone modification

ChIP-seq (P300) What it Measures

Histone modification

3C What it Measures

Transcription co-activator binding

4C What it Measures

One-to-one interactions

Hi-C What it Measures

One-to-many interactions

Capture-C What it Measures

All-to-all interactions

Micro-C What it Measures

Many-to-all interactions

ChIA-PET What it Measures

All-to-all (highest resolution)

HiChIP What it Measures

Many-to-many (with antibody)

LacZ reporter What it Measures

Many-to-many (with antibody)

CAT reporter What it Measures

Functional validation
     Functional validation

DNase-seq Chromatin accessibility (open regions) What it Reveals About Enhancers

Identifies potential regulatory regions (promoters, enhancers)

ATAC-seq Chromatin accessibility (open regions) What it Reveals About Enhancers

Identifies nucleosome-free regions; uses TN5 transposase

MNase-seq Nucleosome positioning What it Reveals About Enhancers

Reveals nucleosome depletion at active regulatory elements

FAIRE-seq Open chromatin (formaldehyde-assisted isolation) What it Reveals About Enhancers

Identifies regulatory elements without crosslinking

ChIP-seq (H3K27ac) Histone modification What it Reveals About Enhancers

Marks active enhancers

ChIP-seq (H3K4me1) Histone modification What it Reveals About Enhancers

Marks primed/active enhancers

ChIP-seq (H3K27me3) Histone modification What it Reveals About Enhancers

Marks poised/repressed enhancers (Polycomb)

ChIP-seq (P300) Transcription co-activator binding What it Reveals About Enhancers

Identifies active enhancer regions

3C One-to-one interactions What it Reveals About Enhancers

Confirms known enhancer-promoter loops

4C One-to-many interactions What it Reveals About Enhancers

Identifies all regions interacting with a locus of interest

Hi-C All-to-all interactions What it Reveals About Enhancers

Genome-wide interaction maps (low resolution)

Capture-C Many-to-all interactions What it Reveals About Enhancers

High-resolution mapping of specific region interactions

Micro-C All-to-all (highest resolution) What it Reveals About Enhancers

Genome-wide enhancer-promoter loops at nucleosome resolution

ChIA-PET Many-to-many (with antibody) What it Reveals About Enhancers

Identifies loops mediated by specific proteins

HiChIP Many-to-many (with antibody) What it Reveals About Enhancers

Enriches for loops involving specific histone marks/TFs

LacZ reporter Functional validation What it Reveals About Enhancers

Tests if a DNA region drives tissue-specific expression

CAT reporter Functional validation What it Reveals About Enhancers

Measures transcriptional activity of regulatory elements