The below mentioned article provides a short note on transcriptomics.
After the genome sequences are being completed, the new questions arise about the functional roles of different genes; the cellular processes in which they participate; mechanism by which the genes regulate the interaction of genes and gene products; changes in level of gene expression in different cell types and states.
To answer all these questions, the new area of science has got emerged which is transcriptomics. The transcription of genes to produce RNA is the first stage of gene expression. Although mRNA is not the ultimate product of a gene, but it is the first step of gene regulation and information about the transcript levels which is needed for understanding gene regulatory networks.
The transcriptome is the complete set of mRNA transcripts produced by the genome at any one time. Unlike the genome, the transcriptome is extremely dynamic, all the cells of an organism contain same genome but the transcriptome varies considerably in different cells at different circumstances due to different patterns of gene expression.
Techniques for Transcriptome Analysis:
High throughput techniques based on DNA chip/microarray technology (i.e., cDNA microarrays, oligo microarrays), cDNA- AFLP (cDNA-amplified fragment length polymorphism) analysis, SAGE (serial analysis of gene expression) and a new technique MPSS (massively parallel signature sequencing) are used for transcriptome analysis.
The cDNA microarray technique is based on the ability of the mRNA molecule to bind specifically to or hybridize to, its original DNA coding sequence in the form of a cDNA template spotted on an array.
DNA chip is prepared on a silicon or glass based surface with regions of known sequence of chosen target DNA, which can hybridize with an unknown labelled DNA sample.
Besides using cDNA clones as probes on an array, oligonucleotides of around 20 nucleotides can also be used as probe. Microarray experiments allow for comparison of gene expression profiles between two mRNA samples (e.g., treatment vs. control, or treatment 1 vs. treatment 2).
The most important advantage of microarray-based technology is that large data sets from different experiments can be combined together in a single database, which allows gene expression profiles from either different samples or samples from different treatments to be compared with each other and analysed together.
Significance of Transcriptomics:
As the transcriptome includes all mRNA transcripts in the cell, it reflects the genes that are being actively expressed at any given time, with the exception of mRNA degradation phenomenon such as transcriptional attenuation. The study of transcriptomics examines the expression level of mRNA in a given cell population.
Many DNA sequences that have been isolated shown to have no known function. However, if they show similar expression patterns to a characterized gene, it is likely that their functions are similar.
It is sometimes possible to identify conserved regulatory sequences of such genes. Ultimately, these studies promise to expand the size of existing gene families, reveal new patterns of coordinated gene expression across gene families and uncover entirely new categories of genes.
Furthermore, the product of any one gene usually interacts with those of many others, therefore, transcriptomics will provide precise knowledge on coordination among genes and their inter-relationships.
It will also help to understand the integration of gene expression and function at the cellular level, revealing how multiple gene products work together to produce physical and chemical responses to both static and changing cellular needs.