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Gene-level Expression Profiling
Gene-level profiling of RNA expression on high-density DNA
microarrays has become a widespread and reliable tool for the analysis of the
transcriptional events underlying the development and progression of disease
and to understand the changes in gene expression leading to a particular drug
response or the altered growth of plants in response to hormone stimuli or
stress. In biomedical research, mRNA expression profiling has been found
particularly useful for the (sub-) classification of complex diseases or the
development of biomarker signatures for diagnostic purposes.
A typical experiment designed to understand the
patho-mechanisms in a particular human disease employs carefully selected
clinical samples that match in age, sex and race to minimize biological
variation in the experimental set-up [1]. Short oligonucleotide probes designed
to match the 3’ terminal part of the corresponding mRNA [2] are immobilized on
a microarray and used to capture labelled mRNA fragments, allowing analysis of
differential gene expression in diseased vs. healthy subjects [3].
Exon-level Expression Profiling
Sequencing
the human genome has revealed that the vast complexity of human cells
is achieved through less than 25,000 coding genes. It has therefore
been concluded that the diversity of the proteome must, to a large
extent, be created by alternative splicing of pre-mRNAs expressed from
individual genes. Recent studies suggested that 40% to 60% of the mRNAs
transcribed from human and mouse genes undergo alternative splicing
and, more recently, a genome-wide survey of mRNA from multiple tissues
using high-density DNA micorarrays estimated the frequencies of
alternative splicing of human genes to be at least 70%.
Alternative splicing is a mechanism for increasing protein
diversity by excluding or including exons during post-transcriptional
processing [1, 2]. Alternatively spliced transcripts are particularly
relevant in the development of complex diseases, such as cancer, as
they may contribute to the etiology of the disease, provide selective
drug targets, or serve as a marker set for diagnosis. While
conventional DNA microarrays for the study of global gene expression
target the 3’ end of the corresponding mRNA molecule, a new generation
of high-density arrays has been designed to interrogate the expression
of more than 1 million individual exon transcripts in the human genome
in a single experiment [3].
Contact CPGR to find out how high-density microarrays can be used to study gene or exon-level expression in humans and how alternative splicing effects development of cells and diseases.
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