78
Body Expression Map of Human Genome
the entire set of genes and their functions
together with control mechanisms written
in the human genome. However, thanks
to the progress of recent molecular biol-
ogy/genetics over the past decade, we now
know that genes are not mere stretches of
nucleotides but are dynamically controlled,
depending on, for example, the develop-
mental stages, and the conditions of the
outer environments of cells or organisms.
Thus, genome-wide mRNA/cDNA analy-
ses were conducted at about the same time
as the major research topic of the Human
Genome Project.
Several different approaches have been
tested and are still in use for these pur-
poses. The Frst approach was to compile
a complete catalog of genes written in
thegenomeofpar
t
icu
larorgan
ismssuch
as human or mouse through a random
collection of expressed cDNA sequences
(expressed-sequence tags, ESTs) from var-
ious tissues. Once as many of these as pos-
sible have been collected, computational
methods involving clustering were used
to compile each of the cDNA fragments
into groups of mRNA sequences, based
on their sequence similarities. In other
wo
rd
s
,theFna
lgoa
lo
fth
i
sk
indo
fap
-
proach is to make a list of entire genes and
their genomic localizations linked with
annotated databases. Recent development
of a high-throughput computational ap-
proach is discussed in the later part of
this chapter.
The second approach has more focus
on the status of expressed genes through
the acquisition of expression proFles of
mRNA/cDNA (body mapping) isolated
from
a
particular
cell
group,
tissue,
or organ. Human body mapping was
Frst started using quantitatively prepared
cDNA libraries constructed from mRNA
isolated from anatomically puriFed cells
or tissues through microscopic dissection,
cell culture, and other cell puriFcation
technologies (±ig. 1). ±or the experimental
details of body mapping, refer to the
previous edition of this encyclopedia. An
alternative approach to determine the
expression proFles is SAGE and DNA
microarrays that will be discussed in
other chapters.
Expression proFling is the only practi-
cal approach to quantify the extent and
to characterize the speciFcities of gene
expression in a particular cell at a spe-
ciFc time, through the identiFcation of
gene signature, elements of gene expres-
sion control, and the network of gene
Gene signature
Mbol
GATC
AAAAA A
AA
A
LLLLL L
LL
L
Fig. 1
Libraries and data collection: All libraries used, harbor only
the 3
0
-terminal cDNA fragments made by digesting vector-primed
cDNA molecules with
Mbo
I (GATC) in order to facilitate the 3
0
-EST
collection and to minimize the difference in cloning efFciencies
among transcripts of different sizes. They were not subjected to
ampliFcation, prescreening, or normalization. Accordingly, the
clonal recurrence roughly represents transcript abundance in this
library.
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