ENCODE element browser and 3D genome browser

Feng Yue, PhD Assistant Professor

Dept. of Biochemistry & Molecular Biology School of Medicine

Penn State University

Outline

1.  Search and visualize ENCODE annotations (gene

expression, candidate promoters, enhancers …)

2.  Visualize ENCODE chromatin interaction data

(Hi-C, ChIA-PET)

ENCODE element query website

ENCODE element query website

Click human tab, and search for the expression for Sox2

Visualize and save the gene expression profile

You can choose the cell types to display!

You can choose the cell types to display!

Linking enhancers to target promoters Enhancer

Bone Marrow Cerebellum Cortex Heart Kidney Liver Lung Mef ES Spleen

Correlation coefficient

Correlation coefficient

DNaseI DNase I DNaseI

Gene 1 Gene 2

Outline for the workshop

1.  Search and download through ENCODE portal

2.  Search and visualize ENCODE annotations (gene

expression, promoters, enhancers …)

3.  Visualize ENCODE chromatin interaction data

(Hi-C, ChIA-PET)

Transcriptional regulation by cis-regulatory elements

Promoter

Co-activator

Enhancer

TF TF

RNA pol Gene transcription

Chromatin conformation capture (3C) experiment

Enhancer

Gene transcription

Promoter

TF TF

Anchor Primer2 primer3 Primer 1

3C experiment

Anchor Primer2 primer3 Primer 1

3C experiment

Hi-C measures genome-wide chromatin interaction

-

_-

_-

_-

_3

0.2

0.25

0.55

0.35

Foxg1

400 kb51000000Chr12

0

40

Normalizedinteraction freq.

Dixon et al. nature, 2012

H3K4me3

RNA polII

CTCF

H3K4me1

Hi-C measures genome-wide chromatin interaction

http://3dgenome.org

Users can query by gene name or genomic loci

Navigation bars to explore Hi-C data

Built-in genome browser session

You can use your own Hi-C data - no need to upload!

Visualize your own Hi-C data

Use virtual 4C to hypothesize the enhancer promoter interaction

Virtual 4C is derived from Hi-C matrix

Jin et al, Nature, 2013

Summary

1.  Search and visualize ENCODE annotations (gene

expression, promoters, enhancers …)

2.  Visualize ENCODE chromatin interaction data

(Hi-C, ChIA-PET)

Acknowledgement

ENCODE consortium ENCODE DCC

- Mike Cherry - Seth Strattan - Ben Hitz - Aditi Kalpagam Narayanan …

ENCODE EDAC - Zhiping Weng …

Yue Lab - Yanli Wang - Lijun Zhang - GalYaroslavsky - Tyler Derr

Dr. Bing Ren

and many others …