E. Bettelli, et al.,
"Reciprocal developmental pathways for
the generation of pathogenic effector
TH17 and regulatory T
cells," Nature, 441(7090):
235-8, 11 May 2006. [Harvard Med. Sch.,
Boston, MA] *040YP
52
1
2
K. Takahashi, et al.,
"Induction of pluripotent stem cells
from adult human fibroblasts by defined
factors," Cell, 131(5):
861-72, 30 November 2007. [Kyoto U.,
Japan; CREST, Kawaguchi, Japan;
Gladstone Inst. Cardio. Dis., San
Francisco, CA] *243MG
41
†
3
M. Wernig, et al., "In
vitro reprogramming of fibroblasts
into a pluripotent ES-cell-like state,"
Nature, 448(7151): 318-24, 19
July 2007. [5 U.S. institutions] *191GC
40
7
4
The ENCODE Project Consortium (E.
Birney, et al.),
"Identification and analysis of
functional elements in 1% of the human
genome by the ENCODE pilot project,"
Nature, 447(7146): 799-816, 14
June 2007. [80 institutions worldwide]
*178FV
39
2
5
P.R. Mangan, et al.,
"Transforming growth factor-ß
induces development of the
TH17 lineage,"
Nature, 441(7090): 231-4, 11
May 2006. [U. Alabama, Birmingham;
NIDCD, NIH, Bethesda, MD] *040YP
38
4
6
A. Barski, et al.,
"High-resolution profiling of histone
methylations in the human genome,"
Cell, 129(4): 823-37, 18 May
2007. [NHLBI, NIH, Bethesda, MD; U.
Calif., Los Angeles] *172FA
38
†
7
D.F. Easton, et al.,
"Genome-wide association study
identifies novel breast cancer
susceptibility loci," Nature,
447(7148): 1087-93, 28 June 2007. [87
institutions worldwide] *183HT
37
†
8
K. Okita, T. Ichisaka, S. Yamanaka,
"Generation of germline-competent
induced pluripotent stem cells,"
Nature, 448(7151): 313-7, 19
July 2007. [Kyoto U., Japan; Japan Sci.
Tech. Agency, Kawaguchi] *191GC
35
5
9
Intl. HapMap Consortium (K.A. Frazer,
et al.), "A second generation
human haplotype map of over 3.1 million
SNPs," Nature, 449(7164):
851-61, 18 October 2007. [72
institutions worldwide] *221LY
31
†
10
Hara, et al., "Suppression of
basal autophagy in neural cells causes
neurodegenerative disease in mice,"
Nature, 441(7095): 885-9, 15
June 2006. [10 Japanese institutions]
*052SL
What do you get when you cross genome-wide mapping with stem-cell
analysis? A very highly cited paper—and the opening of whole new
continents for the cartographers of the genome to explore. At # 5, from
Bradley Bernstein and
Eric
Lander and their colleagues at the Broad Institute of Harvard and MIT,
is a paper that uses a new DNA-sequencing technique to shed light on cell
regulation.
The paper explores the fundamental differences between genetic and
epigenetic changes. Genetic changes, to the DNA itself, are obviously
crucial to the ways in which cells operate, and are passed from generation
to generation. Epigenetic changes affect the way that the DNA is acted on,
and they too can be passed from generation to generation. Most of these
epigenetic changes involve changes in interactions between histones and
other proteins and specific areas of the DNA. The DNA-protein complex is
known as chromatin, and as the DNA wraps around the proteins it forms
structures called nucleosomes that influence the transcription of the DNA.
Other chemical groups attached to the chromatin, often methyl groups on
specific residues, can change the structure of the nucleosome, and
researchers believed that these "marks" were linked to the on-off switches
that determine whether genes are expressed.
One important type of epigenetic change takes place as cells differentiate,
first from embryonic stem cells, which can become any type of cell, to
pluripotent stems cells, which can become any one of a restricted range of
cell types, to the final differentiated cell, which (unless tinkered with)
can only divide into the same type of cell. Another type is known as
epigenetic imprinting; the expression of the gene depends on other genes
that were present in one of the parents. These changes are definitely
linked to changes in the chromatin state of the DNA, but exactly how has
hitherto been a mystery.
Current methods for studying chromatin use an antibody to one of the
proteins to seek out nucleosomes that include that protein.
Chromatin-enriched immunoprecipitation (ChIP) DNA can then be sequenced
using a DNA micro-array. This technique—known as ChIP-chip—is
fine for an individual nucleosome of interest, but it does not scale well,
making it less useful for a genome-wide view of chromatin. Instead, the
Harvard group adopted a new DNA sequencing technique that promises to be
much cheaper and quicker than anything to date. (A paper in Cell
[A. Barski, et al.,, 129(4): 823-7, 2007], by a team led by Keji
Zhao of the National Heart, Lung, and Blood Institute in Bethesda,
Maryland, describing an almost identical approach, narrowly missed the Top
Ten this time around but seems certain to return.)
The sequencing method, developed by Illumina/Solex, attaches single copies
of small random fragments of DNA to spots on a glass surface. These are
then amplified in situ, resulting in a tuft of identical fragments of DNA
at each spot. Fluorescent tags then allow researchers to visualize each
letter in the sequence in turn and finally massive computing power
assembles the millions of tiny fragments into a coherent overall sequence.
The Harvard/MIT group put this new technique, which they call ChIP-seq, to
work on ChIP DNA from three types of cell, representing different levels of
differentiation: embryonic stem cells, neural progenitor cells, and
embryonic fibroblasts. For each, they prepared ChIP samples of histones
with specific marks and for RNA polymerase II, which is involved in
transcribing active parts of the DNA. The end result was 18 chromatin-state
maps.
The Nature paper goes into considerable detail about the many ways
in which the distribution of the different kinds of histone marker seem to
be associated with different kinds of cell. For example, in embryonic stem
cells, gene promoters, especially for "housekeeping" genes, are associated
almost exclusively with one kind of marked histone. In more differentiated
neural progenitor cells and fibroblasts those same markers remain
associated with the housekeeping genes, but a few of the housekeeping genes
are now associated with a different histone marker. In essence, and
oversimplifying drastically, some histone markers are associated with
active genes in undifferentiated cells, other markers are associated with
those same genes, inactivated, in differentiated cells, and some genes
appear to be associated with two different kinds of histone markers. The
researchers suggest that these "bivalent markings" indicate genes that are
"poised for repression" as the cell continues to differentiate. But there
is certainly no simple on-off switch.
The paper discusses many other fundamental aspects of the epigenetic
landscape: different promoters activating the same gene; specific histone
markers associated with the further differentiation of neural progenitor
and fibroblast cells; markers present in some adult tissues and not others.
These, and others, are important contributions. But the real value of the
work surely lies in the new ways it offers of looking at the genome. The
authors end with a shopping list of grand projects. Most will feature on
these pages in due course.
Dr. Jeremy Cherfas is Science Writer at Bioversity International in
Rome, Italy.