Re: Ultraconserved Elements in the Genome: Are They Indispensable?

On 5 Sep, 06:17, "George" <geo...@xxxxxxxxxxxxxxx> wrote:
"Glenn" <GlennShel...@xxxxxxx> wrote in message

news:1188962299.932943.68410@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx



On Sep 4, 7:14 pm, "George" <geo...@xxxxxxxxxxxxxxx> wrote:
http://www.lbl.gov/Science-Articles/Archive/Genomics-ultraconserved.html

BERKELEY, CA - Three years ago, "ultraconserved elements" were
discovered
in the genomes of mice, rats, and humans. These are DNA sequences 200
base
pairs in length or longer - some are over 700 base pairs long - showing
100-percent identity among the three species. They have been perfectly
conserved since the last common ancestor of mice, rats, and humans,
which
lived some 85 million years ago.

These and other highly conserved sequences are thought to have persisted
with little or no change because they are indispensable, performing
functions vital for viability or reproduction. Scientists in the
Genomics
Division of the Department of Energy's Lawrence Berkeley National
Laboratory and DOE's Joint Genome Institute set out to test this
hypothesis
by engineering four different "knockout" mice, each lacking one selected
ultraconserved element.

If truly indispensable, mice lacking an ultraconserved element should
either die or be unable to produce viable offspring. Remarkably, as the
researchers report in the September, 2007 issue of PLoS Biology, the
knockout mice in this study showed almost no ill effects at all.

"For us, this was a really surprising result," says Nadav Ahituv of
Berkeley Lab's Genomics Division and DOE's JGI, a human geneticist who
led
the experiment. "We fully expected to demonstrate the vital role these
ultraconserved elements play by showing what happens when they are
missing.
Instead, our knockout mice were not only viable and fertile but showed
no
critical abnormalities in growth, longevity, pathology, or metabolism."

Edward Rubin, Director of the Joint Genome Institute and Berkeley Lab's
Genomics Division, who directed the study, said, "Many scientists had
speculated that the reason for absolute identity of sequences over the
80
million years since humans and rodents diverged was that these sequences
are crucial for life: if a base changes, the organism would die, so
that's
why we see absolutely no sequence changes in these regions. The results
of
this study clearly show that this is not the case. While I don't think
we
can conclude that the mice we created with the ultraconserved elements
deleted are normal, we can confidently conclude that the presence of the
ultraconserved elements are not required for the viability of the
organism."

Choosing the sequences
Some of the 481 ultraconserved sequences in humans, rats, and mice are
coding sequences, genes that code for proteins, but over half, termed
noncoding ultraconserved elements, are not. Previous studies by the
Berkeley Lab researchers and their colleagues have suggested an
important
role for these noncoding sequences in gene regulation; because they act
to
promote the expression of genes they are known as "enhancers."

For this study the team specifically chose four ultraconserved noncoding
elements, thought to be enhancers of nearby genes that when mutated lead
to
severe developmental abnormalities or fertility problems.

For example, noncoding ultraconserved element number 467 (uc467) has 731
base pairs of sequence that are identical among human, mouse, and rat;
it
is one of the longest of all ultraconserved elements within our genome.
Uc467 is thought to be an enhancer for ARX, a gene that, when defective
in
mice, disturbs male sexual development and causes lethal brain
abnormalities, and in humans causes a wide range of neurological and
sexual-development disorders.

Using standard mouse genetic-engineering techniques, the researchers
prepared four lines of knockout mice, each type lacking one of the
chosen
ultraconserved elements.

"We knew that knocking out the genes themselves leads to lethality or
sexual abnormalities in mice, and sometimes other problems," says
Ahituv.
"So we expected that mice lacking the ultraconserved sequences that are
thought to regulate these genes would produce a similar result:
lethality
or infertility."

Instead of the expected drastic results, however, all four lines
produced
normal litters of healthy mice. Their weight was normal during 10 weeks
of
monitoring; the mice were watched for six months (and by now, many have
been watched much longer) and not only survived but thrived. They were
subjected to numerous clinical assays with no signs of abnormality, and
no
significant differences compared to the wild-type controls.

If not crucial, why conserved?
"There is plenty of evidence that highly conserved sequences do perform
vital functions," says Ahituv. "Indeed, locating noncoding sequences
that
have been unchanged by evolution is one of the main tools scientists use
to
find important functional elements in a genome."

While it's conceivable that conserved sequences are somehow immune to
mutations for reasons that have nothing to do with evolutionary
pressures,
the mechanism of such "sequence armoring" is hard to imagine. The
731-base
pair sequence, uc467, should normally have accumulated some 334
nucleotide
changes in the more than 80 million years that mice, rats, and humans
have
been evolving along separate paths.

Much more plausible is the assumption that these identical DNA sequences
persist because nucleotide substitutions in them would render the
organism
less fit; thus evolution selects against them. So why don't problems
show
up immediately in mice that are missing a conserved sequence?

"Evolution and natural selection do not happen overnight," says Len
Pennacchio, a Berkeley Lab senior scientist who is one of the primary
authors of the study. "The deletion of these elements likely has
relatively
mild effects on fitness that are gradually selected against over time -
several or more generations from when they arise - but not on observable
time scales. The observation is that ultraconserved elements do not
tolerate substitions since their last common ancestor over 80 million
years
ago - but this tells us nothing about when such changes were selected
against. Surely they did occur and were removed on an evolutionary time
scale. Exactly when is not known."

Redundancy is another possibility, says Ahituv, analogous to gene
redundancy that can rescue the organism from expected abnormalities when
vital genes are knocked out. "It may be that we saw no deleterious
effects
in the knockouts because nature provides a backup for these
ultraconserved
elements. We know that for one of the elements we chose, there are other
noncoding ultraconserved elements positioned near it in the genome that
show similar enhancer activity. These may rescue the organism from the
abnormalities we speculated would be caused by the missing
ultraconserved
sequences - though this still does not explain why they are so
ultimately
conserved."

The discovery that deletion of ultraconserved elements does not render
mice
unviable or infertile is a major challenge to our understanding of how
highly conserved elements of the genome persist and what their functions
are, says Ahituv. He and his colleagues are pursuing research aimed at
answering these compelling new questions.

"Deletion of ultraconserved elements yields viable mice," by Nadav
Ahituv,
Yiwen Zhu, Axel Visel, Amy Holt, Veena Afzal, Len A. Pennacchio, and
Edward
M. Rubin, appears in the September, 2007 issue of PLoS Biology and is
available online athttp://dx.doi.org/10.1371/journal.pbio.0050234.

This research was supported by the National Heart, Lung, and Blood
Institute and the National Human Genome Research Institute of the
National
Institutes of Health, and by the Department of Energy.

Berkeley Lab is a U.S. Department of Energy national laboratory located
in
Berkeley, California. It conducts unclassified scientific research and
is
managed by the University of California. Visit our website
athttp://www.lbl.gov.

I'd like to hear the evolutionist explanation for redundant elements
of a system being ultraconserved.
John Harshman, you're an advocate of the "conserved means functional"
belief. Any ideas here?

I'm not a geneticist, but here's my two cents worth - redundancy enhances
survival of the species. Ex - two testicles are better than one (just in
case the unthinkable happens).

George

Having lost a testicle at the age of 13, I'm grateful for the
redundancy. Mind you, considering the fact that my children are all
strong-willed, argumentative, intelligent and ambitious, the rest of
the world may not be so grateful.

RF

.

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