Epigenomic Assays for Dissecting Non-Coding Function

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Epigenomic Assays for Dissecting Non-Coding Function

Epigenomic Assays for Dissecting Non-Coding Function layout 1

what Epigenomic assays are essential for

Epigenomic Assays for Dissecting Non-Coding Function layout 2

ATAC-seq (Assay for Transposase-Accessible Chromatin):

Epigenomic Assays for Dissecting Non-Coding Function layout 3

ChIP-seq (Chromatin Immunoprecipitation):

Epigenomic Assays for Dissecting Non-Coding Function layout 4

CUT&Tag and CUT&RUN

Epigenomic Assays for Dissecting Non-Coding Function layout 5

Hi-C and Chromosome Conformation Capture

Epigenomic Assays for Dissecting Non-Coding Function what Epigenomic assays are essential for

identifying functional non-coding elements
     understanding how variants perturb them.

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): questions 1

what does this assay use

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): questions 2

what does it identify

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): questions 3

what is it used to determine

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): questions 4

example

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): what does this assay use

hyperactive Tn5 transposase

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): what does it identify

to identify regions of open chromatin.

ATAC-seq (Assay for Transposase-Accessible Chromatin):

what is it used to determine

if a disease variant resides in a region accessible to TFs.

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): example

SMARCA4 restoration in ovarian cancer cells was shown to return chromatin accessibility to target promoters using ATAC-seq.

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): full sentence 1

This assay uses a hyperactive Tn5 transposase to identify regions of open chromatin.

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): full sentence 2

It is used to determine if a disease variant resides in a region accessible to TFs.

Epigenomic Assays for Dissecting Non-Coding Function ATAC-seq (Assay for Transposase-Accessible Chromatin): full sentence 3

For example, SMARCA4 restoration in ovarian cancer cells was shown to return chromatin accessibility to target promoters using ATAC-seq.

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  questions1

what does it do

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  questions2

what is H3K27ac

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  questions3

what is H3K27me3

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  questions4

what was this critical for

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  what does it do

ChIP-seq maps regions bound by specific proteins or histone modifications

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  what is H3K27ac

a signature of active enhancers,

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  what is H3K27me3

H3K27me3 marks repressed regions.

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  what was this critical for

identifying the BCL11A erythroid enhancer as a target for sickle cell therapy and dissecting how H3K27M mutations sequester PRC2 activity in pediatric glioblastoma.

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  full sentnece 1

ChIP-seq maps regions bound by specific proteins or histone modifications.

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  full sentence 2

H3K27ac is a signature of active enhancers, while H3K27me3 marks repressed regions.

Epigenomic Assays for Dissecting Non-Coding Function ChIP-seq (Chromatin Immunoprecipitation):  full sentence 3

This was critical in identifying the BCL11A erythroid enhancer as a target for sickle cell therapy and dissecting how H3K27M mutations sequester PRC2 activity in pediatric glioblastoma.

Epigenomic Assays for Dissecting Non-Coding Function CUT&Tag and CUT&RUN questions 1

what are these

Epigenomic Assays for Dissecting Non-Coding Function CUT&Tag and CUT&RUN questions 2

what do they require

Epigenomic Assays for Dissecting Non-Coding Function CUT&Tag and CUT&RUN questions 3

what does this make them ideal for

Epigenomic Assays for Dissecting Non-Coding Function CUT&Tag and CUT&RUN what are these

These are newer, high-resolution techniques

Epigenomic Assays for Dissecting Non-Coding Function CUT&Tag and CUT&RUN what do they require

far fewer cells than ChIP-seq,

Epigenomic Assays for Dissecting Non-Coding Function CUT&Tag and CUT&RUN what does this make them ideal for

studying patient tissue or single-cell clonal heterogeneity.

Epigenomic Assays for Dissecting Non-Coding Function CUT&Tag and CUT&RUN full sentence 1

These are newer, high-resolution techniques that require far fewer cells than ChIP-seq, making them ideal for studying patient tissue or single-cell clonal heterogeneity.

Epigenomic Assays for Dissecting Non-Coding Function Hi-C and Chromosome Conformation Capture:  questions 1

what do these assays do

Epigenomic Assays for Dissecting Non-Coding Function Hi-C and Chromosome Conformation Capture:  questions 2

wwhat does this allow researchers to prove

Epigenomic Assays for Dissecting Non-Coding Function Hi-C and Chromosome Conformation Capture:  questions 3

example

Epigenomic Assays for Dissecting Non-Coding Function Hi-C and Chromosome Conformation Capture:  what do these assays do

These assays map the 3D organization of the genome,

Epigenomic Assays for Dissecting Non-Coding Function Hi-C and Chromosome Conformation Capture:  wwhat does this allow researchers to prove

prove that a distal enhancer variant actually physically contacts and regulates a specific target gene promoter.

Epigenomic Assays for Dissecting Non-Coding Function Hi-C and Chromosome Conformation Capture:  example

Hi-C confirmed the 335kb loop between the rs6983267 SNP and the c-MYC promoter in colorectal cancer.

Epigenomic Assays for Dissecting Non-Coding Function Hi-C and Chromosome Conformation Capture:  full sentence 1

These assays map the 3D organization of the genome, allowing researchers to prove that a distal enhancer variant actually physically contacts and regulates a specific target gene promoter.

Epigenomic Assays for Dissecting Non-Coding Function Hi-C and Chromosome Conformation Capture:  full sentence 2

For instance, Hi-C confirmed the 335kb loop between the rs6983267 SNP and the c-MYC promoter in colorectal cance