The Drug development process - Pharmaceutical Biotechnology: Concepts and Aapplications - page 63

With the exception of knockout animals, these approaches employ, in part at least, sequence
structure/data interrogation/comparison. The availability of appropriate highly powerful compu-
ter programs renders these approaches 'high throughput'. However, even by applying these meth-
odologies, it will not prove possible to identify immediately the function of all gene products
sequenced.
Sequence homology studies depend upon computer-based (bioinformatic) sequence compari-
son between a gene of unknown function (or, more accurately, of unknown gene product function)
and genes whose product has previously been assigned a function. High homology suggests likely
related functional attributes. Sequence homology studies can assist in assigning a putative func-
tion to 40-60 per cent of all new gene sequences.
Phylogenetic profi ling entails establishing a pattern of the presence or absence of the particu-
lar gene coding for a protein of unknown function across a range of different organisms whose
genomes have been sequenced. If it displays an identical presence/absence pattern to an already
characterized gene, then in many instances it can be inferred that both gene products have a
related function.
The Rosetta stone approach is dependent upon the observation that sometimes two separate
polypeptides (i.e. gene products X and Y) found in one organism occur in a different organism as
a single fused protein XY. In such circumstances, the two protein parts (domains), X and Y, often
display linked functions. Therefore, if gene X is recently discovered in a newly sequenced genome
and is of unknown function but gene XY of known function has been previously discovered in a
different genome, then the function of the unknown X can be deduced.
The gene neighbourhood method is yet another computation-based method. It depends upon the
observation that two genes are likely to be functionally linked if they are consistently found side
by side in the genome of several different organisms.
Knockout animal studies, in contrast to the above methods, are dependent upon phenotype ob-
servation. The approach entails the generation and study of mice in which a specifi c gene has been
deleted. Phenotypic studies can sometimes yield clues as to the function of the gene knocked out.
4.4 Genechips
Although sequence data provide a profi le of all the genes present in a genome, they give no infor-
mation as to which genes are switched on (transcribed) and, hence, which are functionally active
at any given time/under any given circumstances. Gene transcription results in the production of
RNA, either mRNA (usually subsequently translated into a polypeptide) or rRNA or tRNA (which
have catalytic or structural functions; Chapter 3). The study of under which circumstances an
RNA species is expressed/not expressed in the cell/organism can provide clues as to the biologi-
cal function of the RNA (or, in the case of mRNA, the function of the fi nal polypeptide product).
Furthermore, in the context of drug lead/target discovery, the conditions under which a specifi c
mRNA is produced can also point to putative biopharmaceuticals/drug targets. For example, if a
particular mRNA is only produced by a cancer cell, that mRNA (or, more commonly, its polypep-
tide product) may represent a good target for a novel anti-cancer drug.
Levels of RNA (usually specifi c mRNAs) in a cell can be measured by well-established tech-
niques such as northern blot analysis or by PCR analysis. However, the recent advent of DNA
microarray technology has converted the identifi cation and measurement of specifi c mRNAs (or