New study provides mechanistic insights into how gene transcription is
regulated in mammalian cells
Mammalian cells pack their genome
into a highly organized three-dimensional structure, in which the thread-like
DNA is wrapped tightly around spool-like proteins. This structure, known as
chromatin, plays an important role in the regulation of gene activity. An
international team of researchers led by Yijun Ruan at the A*STAR Genome
Institute of Singapore1 have now revealed a key mechanism by which the
chromatin regulates gene activity.
Ruan and his co-workers developed
a state-of-the-art sequencing technology called Chromatin Interaction Analysis
with Paired-End-Tag (ChIA-PET), for performing the genome-wide mapping of
long-range interactions between chromatins. The technology looks at different
regions of regulatory DNA sequences including enhancers and promoters, which
regulate gene expression by binding an enzyme called RNA polymerase II
(RNAPII).
The researchers identified
approximately 20 million interactions in their initial analysis. They grouped
these interactions into one of three categories: interactions between promoters
and nearby DNA sequences within the same gene, interactions between promoters
and enhancers (which are located outside the gene on the same chromosome), and
interactions between promoters on different genes.
The researchers found that
interacting genes are not only expressed but also regulated in a co-ordinated
manner. Genetic errors at one gene can propagate to other genes that interact
with it. Ruan and his team believes that their findings can explain why some
genetic diseases exert a wide variety of effects on patients.
The researchers also found that
interactions between promoters could have a combinatory effect. For example,
some weak promoters could function as enhancers to regulate other promoters
through interactions. Ruan and his team suggest that the classical definition
of a promoter may be out of date.
The multi-gene complexes observed
in this study are, in principle, similar to the ‘operons’ found in bacterial
chromosomes. An operon is a cluster of genes whose functions are under the
control of a single promoter.
Scientists have always tried to
understand how the large number of genes in an organism is regulated and
coordinated to carry out the genetic programs encoded in the genome for
cellular functions in mammalian cells. It has been viewed that genes in higher
organisms are individually expressed, while multiple related genes in low
organisms like bacteria are arranged linearly together as operons and
transcribed in single units.
“Our findings show that although
genes in human genomes are located far away from each other, related genes are
in fact organised through long-range chromatin interactions and higher-order
chromosomal conformations,” says Ruan. “The discovery of the mechanism could
open up new understanding in the genetic elements underlying human diseases.”
The A*STAR-affiliated researchers
contributing to this research are from the Genome Institute of Singapore
References
- Li, G., et al. Extensive promoter-centered
chromatin interactions provide a topological basis for transcription
regulation. Cell 148, 84–98 (2012). | article
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