Research led by the Francis Crick
Institute and the Babraham Institute in Cambridge has developed and
used a new technique to join the dots in the genomic puzzle.
Just as a dot to dot puzzle needs
to be completed to visualise the full picture, the researchers'
analysis connected regulatory elements called promoters and
enhancers showing their physical interactions over long distances
within the mouse and human genomes.
The ability to map
promoter-enhancer interactions in the human genome has huge
potential in understanding the genetic basis of disease.
Human development from an embryo
and the establishment of different cell types in the body depends
on a suite of genomic regulatory elements, that orchestrate the
correct expression of genes in different locations and at different
times. To completely understand how a gene is regulated, both in
health and disease, it is necessary to have a comprehensive
catalogue of the regulatory elements that contribute to its
control.
In a paper published in Genome
Research, the scientists refined an existing technique to look at
the million regulatory elements in the mouse genome and link these
to gene promoters to understand how genes are switched on and off.
At the same time, the technique was used to study human blood cell
types. If the genome is imagined as a linear stretch of DNA
sequence, the research pinpointed sections of the genome, where it
loops to bring regulatory elements controlling gene expression into
physical contact with each other. In genomic distances, enhancer
regions can be hundreds of kilobases of DNA letters-A,T,C and G-
(1KB is 1000 letters or bases) away from the genes they
regulate.
Previous interaction assays weren't
able to provide sufficient resolution to link regulatory elements
with specific promoters. To solve this problem, the team at the
Babraham Institute used RNA 'baits' to pull out just the
genomic fragments containing promoters from the melting pot of a
hundred billion genomic interactions in the mouse genome. This
technique is called Promoter Capture Hi-C.
This research served as a proof of
principle for the use of Promoter Capture Hi-C to map genomic
interactions in mouse cells at high resolution.
The human cell analysis, published
in Nature Genetics, presents the most extensive genome-wide map of
promoter-enhancer interactions in the human genome.
Dr Peter Fraser, of the Babraham
Institute said, "These results provide the first genome-wide
catalogue of interactions between gene promoters and their
long-range interacting elements. Previous methods were akin to
analysing a bucket of seawater and using this to make assumptions
on the ocean's contents. With Promoter Capture Hi-C we can trawl
for specific physical associations between regulatory elements that
control gene expression, and use this information to build up a
more complete picture of the genome's three-dimensional shape to
help us understand how this functions in health and disease."
Using the Promoter Capture Hi-C
technique to delve the human genome pinpointed the long-range
interactions of nearly 22,000 promoters, identifying millions of
interactions and providing an unprecedented snapshot of the distal
genomic regions that contact promoters. Genome-wide association
studies (GWAS) have uncovered thousands of specific areas of the
genome (loci) that have been shown to be associated with different
diseases, including within regulatory regions.
Knowing which genes a regulatory
region affects has so far been extremely difficult and this has
been a major roadblock to understanding genome-wide association
studies. The resolution allowed by Promoter Capture Hi-C showed
that the regions that interact with promoters are highly enriched
for DNA mutations (SNPs; single nucleotide polymorphisms) that have
been associated with disease and means that researchers can now
link potentially defective regulatory elements of the genome with
the genes they influence.
Dr Cameron Osborne, from King's
College London (who undertook this research while at the Babraham
Institute) said, "Our data physically ties the GWAS SNPs to
putative gene targets, and shows that they commonly interact with
more distal genes rather than the nearest neighbours. The
identification of GWAS target genes has the potential to unleash a
new phase of characterising polymorphisms and the genes and
molecular pathways they affect."
In addition to linking regulatory
elements to active genes, the analysis in human cells also
identified connections with inactive genes and elements that appear
to function as transcriptional silencers. A lot less is known about
what switches genes off compared to our understanding of what
switches them on. The characterisation of such elements may help to
define a genomic signature for silencer elements, allowing them to
be more easily identified throughout the genome. Ultimately, this
may shed light on the mechanisms which suppress gene
expression.
The pluripotent regulatory circuitry connecting promoters to their
long-range interacting elements is published in Genome
Research and Mapping long-range promoter contacts in human cells with
high-resolution capture Hi-C is published in Nature
Genetics.