New route for heredity bypasses DNA

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New route for heredity bypasses DNA

http://www.eurekalert.org/pub_releases/2008-01/pu-nrf010408.php

A group of scientists in Princeton's Department of Ecology and

Evolutionary Biology has uncovered a new biological mechanism that

could provide a clearer window into a cell's inner workings.

What's more, this mechanism could represent an " epigenetic " pathway -

- a route that bypasses an organism's normal DNA genetic program --

for so-called Lamarckian evolution, enabling an organism to pass on

to its offspring characteristics acquired during its lifetime to

improve their chances for survival. Lamarckian evolution is the

notion, for example, that the giraffe's long neck evolved by its

continually stretching higher and higher in order to munch on the

more plentiful top tree leaves and gain a better shot at surviving.

The research also could have implications as a new method for

controlling cellular processes, such as the splicing order of DNA

segments, and increasing the understanding of natural cellular

regulatory processes, such as which segments of DNA are retained

versus lost during development. The team's findings will be

published Jan. 10 in the journal Nature.

Princeton biologists Landweber, Mariusz Nowacki and Vikram

Vijayan, together with other members of the lab, wanted to decipher

how the cell accomplished this feat, which required reorganizing its

genome without resorting to its original genetic program. They chose

the singled-celled ciliate Oxytricha trifallax as their testbed.

Ciliates are pond-dwelling protozoa that are ideal model systems for

studying epigenetic phenomena. While typical human cells each have

one nucleus, serving as the control center for the cell, these

ciliate cells have two. One, the somatic nucleus, contains the DNA

needed to carry out all the non-reproductive functions of the cell,

such as metabolism. The second, the germline nucleus, like humans'

sperm and egg, is home to the DNA needed for sexual reproduction.

When two of these ciliate cells mate, the somatic nucleus gets

destroyed, and must somehow be reconstituted in their offspring in

order for them to survive. The germline nucleus contains abundant

DNA, yet 95 percent of it is thrown away during regeneration of a

new somatic nucleus, in a process that compresses a pretty big

genome (one-third the size of the human genome) into a tiny fraction

of the space. This leaves only 5 percent of the organism's DNA free

for encoding functions. Yet this small hodgepodge of remaining DNA

always gets correctly chosen and then descrambled by the cell to

form a new, working genome in a process (described as " genome

acrobatics " ) that is still not well understood, but extremely

deliberate and precise.

Landweber and her colleagues have postulated that this programmed

rearrangement of DNA fragments is guided by an existing " cache " of

information in the form of a DNA or RNA template derived from the

parent's nucleus. In the computer realm, a cache is a temporary

storage site for frequently used information to enable quick and

easy access, rather than having to re-fetch or re-create the

original information from scratch every time it's needed.

" The notion of an RNA cache has been around for a while, as the idea

of solving a jigsaw puzzle by peeking at the cover of the box is

always tempting, " said Landweber, associate professor of ecology and

evolutionary biology. " These cells have a genomic puzzle to solve

that involves gathering little pieces of DNA and putting them back

together in a specified order. The original idea of an RNA cache

emerged in a study of plants, rather than protozoan cells, though,

but the situation in plants turned out to be incorrect. "

Through a series of experiments, the group tested out their

hypothesis that DNA or RNA molecules were providing the missing

instruction booklet needed during development, and also tried to

determine if the putative template was made of RNA or DNA. DNA is

the genetic material of most organisms, however RNA is now known to

play a diversity of important roles as well. RNA is DNA's chemical

cousin, and has a primary role in interpreting the genetic code

during the construction of proteins.

First, the researchers attempted to determine if the RNA cache idea

was valid by directing specific RNA-destroying chemicals, known as

RNAi, to the cell before fertilization. This gave encouraging

results, disrupting the process of development, and even halting DNA

rearrangement in some cases.

In a second experiment, Nowacki and Yi Zhou, both postdoctoral

fellows, discovered that RNA templates did indeed exist early on in

the cellular developmental process, and were just long-lived enough

to lay out a pattern for reconstructing their main nucleus. This was

soon followed by a third experiment that " … required real chutzpah, "

Landweber said, " because it meant reprogramming the cell to shuffle

its own genetic material. "

Nowacki, Zhou and Vijayan, a 2007 Princeton graduate in electrical

engineering, constructed both artificial RNA and DNA templates that

encoded a novel, pre-determined pattern; that is, that would take a

DNA molecule of the ciliate's consisting of, for example, pieces 1-2-

3-4-5 and transpose two of the segments, to produce the fragment 1-2-

3-5-4. Injecting their synthetic templates into the developing cell

produced the anticipated results, showing that a specified RNA

template could provide a new set of rules for unscrambling the

nuclear fragments in such a way as to reconstitute a working nucleus.

" This wonderful discovery showed for the first time that RNA can

provide sequence information that guides accurate recombination of

DNA, leading to reconstruction of genes and a genome that are

necessary for the organism, " said Meng-Chao Yao, director of the

Institute of Molecular Biology at Taiwan's Academia Sinica. " It

reveals that genetic information can be passed on to following

generations via RNA, in addition to DNA. "

The research team believes that if this mechanism extends to

mammalian cells, then it could suggest novel ways for manipulating

genes, besides those already known through the standard methods of

genetic engineering. This could lead to possible applications for

creating new gene combinations or restoring aberrant cells to their

original, healthy state.

Support for the team's research was provided by the National Science

Foundation, the National Institutes of Health and the School of

Engineering and Applied Science senior thesis research fund.