Researchers at UCL (University
College London) have discovered a new mechanism for
'splicing-based' gene regulation, with possible implications for
Most of our genes contain introns
and exons. After the genes are transcribed into RNA, the introns
are removed by 'splicing' and exons are joined together to form a
messenger RNA (mRNA), which contains the instructions for making a
protein. In this study the scientists found that cells sometimes
select a piece of a gene as an exon, but later discard it, in a
process called recursive splicing.
They observed this process
happening in some of the longest genes that are expressed in the
brain, which are often implicated in autism or other
neurodevelopmental disorders. The process is coordinated by
so-called 'recursive sites', which are highly conserved in mammals,
and in one case even from fish to humans.
Likening the process to making a
film, Professor Jernej Ule, who led the research with Dr Vincent
Plagnol (both of UCL) said: "Our genes are like a raw footage for
film. Just like the individual shots are combined into the motion
picture, the exons are selected and combined into the mRNA.
"We show that most of the longest
genes in our genome are primarily expressed in the brain. The brain
appears to be a very demanding director, which needs an
extraordinary amount of raw footage and special mechanisms like
recursive splicing to produce the motion picture."
Long introns in genes contain
hundreds of so-called 'cryptic sequences', which could be used to
direct the splicing process. This means that the cellular machinery
faces great challenges in distinguishing true exons from those that
that appear very similar to exons, but are not supposed to be
The scientists used a technique
called high throughput DNA sequencing to identify many previously
unobserved splicing events within long introns. They then examined
the mechanisms that distinguish genuine splice sites from cryptic
Surprisingly, the study found that
some of the cryptic splice sites are actually highly used and
authentic splice sites, even though they have not been discovered
before. This led to discovery of recursive sites that are present
deep within extremely long introns. The scientists found that a
recursive site is initially defined as an exon, but is later
removed, allowing it to remain invisible.
"However, if the recursive site is
preceded by other cryptic splicing events, then the exon is not
removed - creating a 'binary switch' or checkpoint that can
distinguish correct splicing events from the newly emerging cryptic
events, which could be potentially damaging," explained Dr
Christopher Sibley, also of UCL.
Professor Ule said: "Even though
cryptic splicing is often damaging, it allows new exons to emerge,
which plays an important role in the rapid evolution of the brain.
Long introns increase the frequency of cryptic splicing.
"Thus, long introns on one hand
enable evolutionary tinkering, whereas recursive splicing ensures
that this tinkering does not disturb the primary mRNA that needs to
be made from the gene."
"This study is an important step
towards understanding the role of non-coding elements in genes,"
added Dr Plagnol. "Accordingly, attention should be paid to these
sites in future studies of disease-causing mutations, especially
for brain-related disorders, as this is the organ where these long
genes are predominantly expressed."
The paper, Recursive splicing in long vertebrate genes, is
published in Nature.