Note: Track Released Nov. 27, 2019
The ENCODE project has established an epigenomic resource for mammalian development,
profiling a diverse panel of mouse tissues at eight developmental stages from 10.5 days post
conception until birth.
This track set presents enhancer-promoter interactions
predicted from correlation of enhancer-associated chromatin signals and gene expression
across tissue stages, based on histone modification (ChIP-seq)
and transcription (RNA-seq) assays and analysis performed by the ENCODE project.
Data underlying this track are presented in the
Histone Modifications and
tracks, part of the ENCODE
The promoters presented in this track were derived from experimentally validated promoters
provided by the Eukaryotic
Promoter Database (EPDNew). A more complete presentation of this annotation can be found in the
EPDnew Promoters track.
Display Conventions and Configuration
This track is a multi-view composite track containing four data types (views):
- Putative enhancer elements
- Gene promoters
- Predicted interactions between enhancers and gene
- Clustered interactions, by gene or enhancer
For each view, there is a choice of two subtracks to display individually on the browser; the full
set of interactions (and component promoters and enhancers), and a more stringent set, containing
only interactions replicated in two biological replicates. Instructions for configuring multi-view
tracks are here.
The display aims to improve distinguishing genes and their interactions by coloring successive genes
in different colors. All interactions with a gene are colored the same as the gene promoter.
The promoter display follows EPD conventions; the "thin" part of the item represents the
49 bp upstream of the annotated transcription start site (TSS) whereas the "thick" part
represents the TSS plus 10 bp downstream. The relative position of the thick and thin parts define
the orientation of the promoter.
Strong enhancer calls from ChromHMM were merged and filtered to produce a set
of 66,556 putative strong TSS-distal enhancers across all tissues and developmental stages,
and H3K27ac signals at these regions were quantified using uniquely aligned,
de-duplicated ChIP-seq reads.
Topologically associated domains (TAD's) identified in mouse ES-cells (Dixon et al.) were
then used to constrain enhancer/gene associations.
All protein-coding genes and putative strong enhancers within each TAD were evaluated in
terms of the Spearman's correlation (SCC) between the H3K27ac pattern of enrichment and
the mRNA expression from RNA-seq across samples.
The SCC of each enhancer was calculated with reference to all genes on the chromosome, and this
metric was used to estimate p-value by two strategies.
Putative enhancers showing a p-value <= 0.05 (from both strategies)and a SCC >= 0.25
Two maps were independently derived from two biological replicates of ChIP-seq and RNA-seq data.
The "All" dataset contains significant interactions present in either biological
replicate. The "Replicated" dataset contains significant interactions present in both
Detailed methods can be found in Gorkin et al, in References below.
Promoters and Interactions
The Promoter subtrack was generated at UCSC. EPDnew mouse promoter release 003 (June 2018) was
obtained from obtained from the
Eukaryotic Promoter Database,
and filtered to contain only promoters appearing in the Enhancer/Gene maps.
The Interactions view was generated at UCSC from the Enhancer/Gene maps by linking the enhancers
to promoter regions based on the EPDnew promoters.
Multiple promoters for a single gene
were merged into a single region covering the range of all promoters.
Histone ChIP-seq and RNA-seq data underlying this annotation are available from the
The EPDnew promoters for mouse can be downloaded from the
EPD FTP site.
Thanks to Iros Barozzi and colleagues in the
Environmental Genomics and
Systems Biology Division at the Lawrence Berkeley National Laboratory for generating the
enhancer/gene association analysis and to David Gorkin and Yanxiao Zhang at the Ren lab
(UCSD/Ludwig Institute for Cancer Research) for providing these data and assisting with track
development at UCSC.
Gorkin et al. An atlas of dynamic chromatin landscapes in the developing mouse fetus.
Nature, In Press. (pre-print: doi:
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee
BT et al.
ENCODE data at the ENCODE portal.
Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32.
PMID: 26527727; PMC: PMC4702836
Dreos R, Ambrosini G, Groux R, Cavin Périer R, Bucher P.
The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.
Nucleic Acids Res. 2017 Jan 4;45(D1):D51-D55.
PMID: 27899657; PMC: PMC5210552
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.
Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Nature. 2012 Apr 11;485(7398):376-80.
PMID: 22495300; PMC: PMC3356448