[Cangen-L) Histone Code

http://www.eurekalert.org/pub_releases/2001-08/cshl-cj080601.php
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Researchers Focus on Histone Code
Studies offer support for an emerging hypothesis

By Brendan A. Maher


Histones, the proteins around which DNA coils to form chromatin, are moving 
toward
the forefront of epigenetic research (see also, "The Meaning of Epigenetics"). A
recently floated hypothesis states that the highly modifiable amino termini, or
tails, of these proteins could carry their own combinatorial codes or signatures
to help control phenotype, and that parts of this code may be heritable.
Histones are perhaps more intimately linked with DNA than any other protein.
Transcriptional regulation, recombination, repair, and replication--basically
anything that happens to the DNA--must happen within the context of its 
packaging.
That alone lends importance to the field. Leukemia therapeutics based on
inhibition of histone modifiers have already made it to the clinic.1 And in 
light
of this new "histone code" hypothesis, researchers are quick to tout further
possibilities in human development, fertility, and other types of cancer. 
Shelley
L. Berger, associate professor of molecular genetics at the Wistar Institute,
University of Pennsylvania, says, "I think it's going to be really critical in
human biology. It's not just some dry academic pursuit."

Though first voiced in 1993 by Bryan Turner, professor of experimental genetics,
University of Birmingham Medical School, Birmingham, U.K.,2 the histone code
hypothesis was formally named last year by C. David Allis, Byrd professor of
biochemistry and molecular genetics, University of Virginia Medical School, and
his postdoc, Brian Strahl.3

Before the new hypothesis, the reigning theory had stated that modifications 
like
acetylation and phosphorylation alter the electrostatic charge of histone tails,
thereby loosening their grip on the DNA. While not excluding old assumptions, 
the
new hypothesis states that specific modifications, like acetylation,
phosphorylation, or methylation, to specific amino acid residues on histone 
tails
facilitate processes by forming combinatorial codes that other proteins read.
According to Allis, modification patterns might form a sort of landing pad upon
which specialized regulatory proteins dock. Birth of this notion came from
observations that the same modification could bring about different regulatory
outcomes depending on where it appears on the histone tails. A case in point, 
says
Allis, are the recent indications that the distinct methyl marks occurring only 
a
few amino acids away from each other are associated with transcriptionally 
active
euchromatin or unexpressed heterochromatin. "It has such a wonderfully split
personality that it really makes you think about a code," Allis says.

Though intentionally vague, the hypothesis finds support in recent Science
articles.4-5 Berger and her lab found that in budding yeast, a certain
phosphorylation event on the histone H3 tail is required for acetylation at a
different amino acid on the same tail. Further, the kinase that phosphorylates 
at
one promoter sequence does not necessarily phosphorylate at others.4 Berger 
says,
"The very clear establishment of that pattern leads to support for the idea that
there is a code, a histone code, and that the modifications vary at different
places in the genome and are doing very specific things to regulate
transcription."

For the past five years--basically since the first histone acetyltransferase and
histone deacetylases were found,1 acetylation has been a hot research topic. 
Now,
say Allis and others, methylation is coming into its own. Because methyl groups
are relatively stable and there is yet no known histone demethylase to remove 
the
marks, histone methylation, which can activate or silence a gene, is believed to
pass its signature on to daughter cells. In a nontransient form of histone
modification, it's possible, says Turner, "to maintain a particular gene
expression pattern--either on or off--over a long period."

Berger explains, "The methyl transferase enzymes actually have domains... that
recognize the methylated histone. Why would you need that? Well, it would allow
you to provide a heritable mark." Allis points out that methylation at one amino
acid coincides quite thoroughly with X inactivation in sex determination and the
phenomenon of gene imprinting.

Shiv Grewal, assistant professor of molecular biology and genetics at Cold 
Spring
Harbor Laboratory, showed that differential sites of histone H3 methylation mark
active and inactive regions of the chromosomes in fission yeast to establish a
specific histone code.5 In inactive heterochromatic regions, histone H3 tails 
were
specifically methylated at lysine 9, and in the adjacent active region, the 
tails
were methylated at lysine 4 only a few amino acids away. Specific DNA sequences
stand in between different chromatin neighborhoods. When Grewal's lab mutated 
the
boundaries, the methlyation pattern associated with heterochromatin spread past
them, silencing formerly expressed genes. "You have implications," Grewal says,
"not only at the molecular level, but at a cellular level ... and all the way up
to population biology."

Yet with four different histone proteins, each with between 10 and 30 amino acid
residues on their N-termini, along with numerous other types of histone
modifications like ubiquitination and ADP-ribosylation, researchers are just
beginning to unravel this mystery. For now, the limitations lie in the 
technique.
Chromatin Immunoprecipitation (ChIP) is really the only tool researchers have 
for
examining these ideas, says Turner. "Advances in this area are going to depend 
on
advances in the chromatin immunoprecipitation approach," he says. And, while
leaders in the field will continue to be those who are best equipped to produce
the antibodies, new technologies could aid in moving the field forward.

Grewal notes that some are moving toward amalgamating the advances in ChIP with
advances in microarray technology, "So we have what we call, 'ChIP on a chip." 
He
believes that in 10 years, scientists will have a clearer picture of the kind of
epigenetic map the histone code could make up. But don't wait for a Rosetta 
stone,
Turner cautions. This will not be static like the genetic code, he says, but
something that is context-dependent--meaning different things in different
situations. "I think the potential is enormous," Turner says. The genome,
relatively small in size, is just the starting point. "What matters is how you 
use
it."

References
1. E. Russo, "Hot Papers in acetylation," and "Hot papers in deacetylation," The
Scientist, 13[5]:13, March 1, 1999.

2. B.M. Turner, "Decoding the nucleosome," Cell, 75[1]:5-8, 1993.

3. B.D. Strahl and C.D. Allis, "The language of covalent histone modifications,"
Nature, 403:41-5, Jan. 6, 2000.

4. W. Lo et al., "Snf1--A histone kinase that works in concert with the histone
acetyltransferase Gcn5 to regulate transcription," Science, 293:1142-6, Aug. 10,
2001.

5. K. Noma et al., "Transitions in distinct histone H3 methylation patterns at 
the
heterochromatin domain boundaries," Science, 293:1150-55, Aug. 10, 2001.
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Translating the Histone Code: A Tale of Tails at Stetten Talk

By Alison Davis

News stories appearing over the last year would have everyone believe that
scientists have ? once and for all ? cracked the human genetic code. Indeed, two
teams of scientists have already published a draft sequence of our 
3-billion-unit
jumble of DNA "letters." But the task of thoroughly deciphering the code's
protein-making instructions ? something our bodies do with ease all the time ? 
is
a complicated puzzle that will keep researchers busy for decades to come. Dr. C.
David Allis of the University of Virginia will be narrating the latest chapter 
on
how our cells translate pieces of DNA into a meaningful message at this year's
DeWitt Stetten Jr. Lecture. Allis will describe his research untangling the
functions of chromatin, structures inside our cells that package genes. The talk
will be held on Wednesday, Oct. 17 at 3 p.m. in Masur Auditorium, Bldg. 10.

Allis is a pioneer in research that aims to clarify how cells contain and 
protect
their most precious cargo, DNA, in protein-rich assemblies that are collectively
called chromatin. In a sense, chromatin acts as a gatekeeper for our genes,
regulating access to DNA by cellular equipment that decodes genes.

 Dr. C. David Allis

His groundbreaking studies have begun to reveal that a key step in how cells
interpret their genetic code involves actually finding certain genes inside
chromatin. A cell's gene-decoding machinery is drawn to proteins in chromatin 
that
have been "marked" with a variety of natural chemical tags. Putting on these 
tags
and taking them off, Allis has found, is a critical aspect of targeting a cell's
gene-reading activities.

In recent years, Allis' lab has helped to discover several of the cellular 
systems
that carefully balance the chromatin-marking chemical tags, called acetyl,
phosphate and methyl groups. These units get attached to histones, the principal
protein building blocks of chromatin that wind DNA into a protective spool. For
example, he explains, the "aurora kinase" enzyme puts a tag called a phosphate
group at a particular spot on the ends, or "tails," of histone proteins. 
According
to Allis, this tag somehow tells the cell that it is time to bundle up its
chromatin in time for cell division. This process helps to ensure that the 
cell's
genetic material is separated precisely in half during cell division.

By conveying such a message, genes get turned on ? or in some cases, off ? Allis
says. In the case of cancer cells, inappropriate control of certain growth genes
can fuel unchecked cell division. According to Allis, the "chromatin link" to
cancer is just now beginning to be appreciated. Indeed, his studies have 
uncovered
that several histone-marking enzymes, like the aurora kinase, actually are 
revved
up in cancer cells, making them an important target for developing future cancer
drugs.

Allis first got interested in chromatin more than 20 years ago, while working 
as a
postdoctoral fellow in the lab of Dr. Martin Gorovsky at the University of
Rochester. Then and now, Allis has remained committed to studying chromatin via
model systems such as the protozoan Tetrahymena, a single-celled ciliate 
organism
that he refers to as an "offbeat pond-water beast."

Offbeat or not, it's also the organism that netted another NIGMS grantee, Dr.
Thomas Cech of the University of Colorado at Boulder and the Howard Hughes 
Medical
Institute, the 1989 Nobel prize in chemistry ? for figuring out that the genetic
material RNA can work as an enzyme.

Scientists like Allis, Cech and countless others use so-called lower organisms
like Tetrahymena to address fundamental questions that pervade biology. Such
systems are simple, but they retain important similarities to the workings of
animal and human cells.

"Forget about what you do in the lab, look at what nature did," says Allis, 
citing
the molecules and cellular processes that recur over and over again throughout 
the
biological kingdom.

He says he is extremely grateful for years of NIH funding to work with "offbeat"
model organisms. "The implications for human biology and disease are
far-reaching," he says.

Allis earned a bachelor's degree in biology from the University of Cincinnati in
1973 and a doctorate in biology from Indiana University in 1978. He was on the
faculty at Baylor College of Medicine from 1981 to 1990, at Syracuse University
from 1990 to 1995, and at the University of Rochester from 1995 to 1998. Since
1998, he has been the Harry F. Byrd, Jr. professor of biochemistry and molecular
genetics, professor of microbiology, and member of the Center for Cell Signaling
at the University of Virginia Health Sciences Center. He has won several awards
for both teaching and research, and is an elected member of the American Academy
of Arts and Sciences.

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