Transcriptomics as a Powerful Tool in Understanding Gene Expression - Essay Example

Running head: TRANSCRIPTOMICS AS A TOOL IN UNDERSTANDING GENE EXPRESSION Transcriptomics as a powerful tool in understanding gene expression Name Course Institution December 9, 2010 Transcriptomics as a Powerful Tool in Understanding Gene Expression Introduction Transcriptomics is the study of the transcriptome; it is the section in molecular biology that involves the study of the messenger RNA molecules, originating from an individual or population of a particular cell type Transcriptome is further defined as the complete set of RNA transcripts and molecules produced by the genome at a time. A transcriptome is dynamic and changes under different circumstances because of the different patterns of gene expression. It is also the initial product of genome expression. The transcriptome is a combination of all RNA molecules that includes mRNA, rRNA, tRNA, and other RNA that is non-coding and produced in one or a population of cells. This term can be also be used to mean the total set of transcripts that are contained in a given organism, or to a particular subset of transcripts that are present in a particular cell type. Varying from the genome which is roughly embedded in a given cell line without mutations, transcriptome varies with external environmental conditions because it involves all mRNA transcripts in the cell, transcriptome elicits the genes that are expressed actively at any given time, with the exclusion of mRNA degradation situations for example the transcriptional attenuation. Discussion The study of transcriptomics can also be regarded as expression profiling because it examines the expression level of mRNAs for a given cell population. It often use high-throughput methods based on DNA micro array technology and the application of next-generation sequencing technology in the study of the transcriptome at the nucleotide level is known as RNA-Seq (Tarca, Cooke, and Mackay, 2005). A genome can be defined as a store of biological information, only that it cannot release the information to the cell on its own then a transcriptome being a collection of RNA molecules derived from protein-coding genes whose biological information is required by the cell at a particular time becomes a tool for genome expression. RNA molecules take the responsibility of directing synthesis of the proteome. The proteome is the final product of genome expression which is the cell’s repertoire of proteins and specifies the nature of the bio-chemical react ions that the cell is able to carryout at any particular time. The flow chart below shows how information is expressed by the genome from the proteome to the transcriptome (Ikeo, 2003). GENOME. TRANSCRIPTOME. (RNA copies of the active protein-coding gene) PROTEOME. (The cells repertoire of proteins) Transcriptome are formed by a process known as transcription. Transcription is a process in which individual genes are copied into RNA molecules. A proteome is formed by a process which involves translation of the RNA molecules into proteins; this process of transcription and translation is the expression of individual genes is described simply as the two-step process (“DNA makes RNA makes proteins”). These two steps are brought about by the idea of synthesis of RNA from the DNA molecules. During the synthesis of RNA, DNA dependent RNA polymerase enzymes are responsible for transcription of DNA to RNA (Ihaka, and Gentleman, 1996). This involves an enzymatic reaction in which the above named enzymes catalyses resulting into polymerization of RNA from rib nucleotides and occurs in a DNA dependent manner meaning that the sequence of nucleotides in a DNA template dictates the sequence of nucleotides in the RNA which is made. This process affects the contents of RNA produced or synthesized. It should however be noted that not all of RNA constitutes the transcriptome. It is only the coding RNA that constitutes the transcriptome because it is constituted of the molecules that have been transcribed from protein-coding genes and which are capable of being translated into protein. There are two types of RNA; the coding and non-coding RNA (Hegde, 2000). Coding RNA comprises of the transcriptome and is made up of one class of molecule. This is called the messenger RNA (mRNA) which is transcripts of protein coding genes and hence is translated into protein in the latter stages of genome expression; mRNA’s are short lived and make up to like 4%of the total RNA and are degraded soon after synthesis. This means that the composition of the transcriptome is not fixed and can be restructured by changing the rate of synthesis of individual Mrna. On the other hand, non-coding RNA’s are diverse. It comprises of transcripts with a number of different functions, all of which are performed by the RNA molecule themselves. The prokaryotes and eukaryotes the two main types of non coding RNA are: ribosomal RNA,(rRNA) This are most abundant in the cell and they make over 80% (Fedorova, 2002). They are components of ribosome’s (ribosome’s are the structures on which protein synthesis occurs). Transfer RNA’s (tRNA) are the second type and are small molecules that are also involved in protein synthesis and they carry amino acids to the ribosome and ensure that these are linked together in the order specified by the nucleotide sequence of the Mrna that is being translated. The other non- coding RNA types are limited in their distribution, unlike ribosomal and transfer RNA which are present in the cells of all species. These ones include, small nuclear RNA (snRNA), small nucleaollar rna (snRNA), small cytoplasm RNA (scRNA). These are named according to here they are located and in close relation to their function. In the understanding of these cells, there are several differences between normal cells an cancer cells which makes cancer cells more powerful than normal cells. Cancer is a health problem that is very common in the contemporary world and it results from changing lifestyles that comprises intake of unhealthy food, exposure to environments that triggers cancer due to human activities and other factors that promotes the development of cancer (Swertz, and Jansen, 2007). In medical terms, it is known as malignant neoplasm, which is a category of diseases in whereby a cell or a group of cells exhibits growth which is not controllable or mutation that is not normal and surpasses the limits then this phenomenon intrudes and destroys the system of adjacent tissues, and sometimes can result in the spreading to other parts of the body via lymph or blood a situation called metastasis (Eppig, Blake, Bult, Kadin, Richardson, and Group, 2007). These situations of malignant condition of cancers distinguish them from benign tumors that are self-limited, and do not intrude or spread to other location of the body. Majority of cancers form a tumor but some, like leukemia, do not. The section of human medicine that is concerned with the research, treatment, and diagnosis and prevention of cancer is known as oncology (Eisen, Spellman, Brown, and Botstein, 1998). The significance of micro array-based technologies, which is the concept in transcriptomics, helps a lot in the process of characterizing tumors at both the proteomic and genomic stages, which have greatly revolutionized the endeavors and efforts in oncology, which particularly deals with the amelioration and prevention of cancer. Transcriptomic gene expression profiling of various human tumor tissues has enabled doctors and researchers to the identify the expression patterns in order to comprehend the disease outcome and the probability of drug resistance, also has helped in the discovery of new therapeutic techniques and built insights into disease pathogenesis. The Protein micro array technologies, including the reverse-phase protein arrays, give a unique opportunity to profile tissues and ascertain the activities of signal pathways within isolated cell populations. The essence of transcriptomics enhances a technology that can be utilized in the process, identifying patients who are likely to benefit from specific treatment modalities and aid in monitoring therapeutic responses in samples obtained during and after treatment (Edgar, Domrachev, Lash, 2002). Constant application of proteomic and genomic, micro array technologies in clinical practice will require concerted efforts to standardize the methodologies, controls and standards, and analytical tools used which are the main concerns in transcriptomics. Elaborate and , independent validation using large, statistically databases are also necessary which involves integration of concomitant genomic and proteomic-based molecular profiling techniques are also capitalized in the diagnosis and treatment of cancer which clearly shows the significance of transcriptomics in oncology. As discussed above, mRNA transcript expression profiling gives an effective dimension to various kinds of research especially in cancer research. This approach enables the researchers to comprehend more about the cell’s transcription of activated genes. Transcriptomics is the science of determining the transcript expression of the cells hence important greatly helps in the in advanced management of cancer in the post genome level. Some of the side applications of transcriptomics are in the actual cancer diagnostics and treatment according to tumor gene expression profiling of mRNA and also the application of biomarker in discovering and development of drugs. There is less than 2% of the mammalian genome that encodes proteins therefore not much of gene will be transcribed to RNA. Yet, the fraction of transcribed gene is still significant. Recently, there is a lot of research and studies about the microRNA that have been carried out in trying to understand to understand more about tumor genesis and some studies have shown that the microRNAs have high potential in diagnostic and treatment role. Therefore, these endeavors and efforts involve application of transcriptomics and Cancer can affect everyone across all age brackets but people with increased ages are more vulnerable. Approximately 13% of all human deaths in the year 2007 that translates to around 8million people in the globe died because of cancer related problems. Cancers has been often regarded as an environmental disease with higher percentages of cases attributed to lifestyle of the people and environmental factors and a small percentage due to complexities in genetics. The common factors that results to deaths from cancer includes tobacco in take, poor diet and overweight and obesity related complications, infections from cancerous objects, effects of radiation, poorly managed stress, pollution, limited physical exercise among others.. These issue results in the dysfunction of genetic materials of crucial cells which translates to genetic abnormalities which affects the functioning of two general classes of genes and activates cells called oncogenes which is cancer promoting by enhancing its growth which is rapid and facilitates its division (Eaton, 2006). This phenomenon will result in the deactivation of tumor suppressor genes in the cancer cells, hence, interruption on its normal functioning, for example, in the accurate replication of DNA, the order of the cell cycle and the general coordination with the immune system hence the advent of cancer transcriptomics has a helpful field in the research, study, diagnosis and treatment of cancer because, unlike normal cells, cancer cells can grow without dying meaning that they are so dangerous. Researchers have spend sleepless nights in the laboratories trying to find r a ways of killing cancer cells and some have developed ways in which cancer cells can age and die which could lead to treatment of cancer by slowing or stopping the rate of growth of tumors through the frameworks of transcriptomics A notable clear difference between cancer and normal cells is that cancer cells can divide forever and live forever, meaning that they are immortal but for normal cells, they will divide for a number of times and stop growing hence they get old and die or become dormant. Cancer cells have a unique way of maintaining their telomere; their telomere doesn’t get shortened but each time the normal cells divide, they lose some telomere in their DNA sequence which eventually results in the telomere becoming too short and stops growing. In summary, a telomere is a region of repetitive e DNA at then end of a chromosome and it protects the end of the chromosome from deterioration Telomere regions deter the degradation of genes near the ends of chromosomes by allowing for the shortening of chromosomes ends, which occurs during replication of chromosomes. Telomere shortening mechanisms normally limits cells to a fixed number of division sand this mechanism is responsible for the aging on the cellular level and sets a limit on the cells lifespans. These are disposable buffers blocking the ends of c chromosomes and are consumed during cell division. They are replenished by an enzyme called telomerase. Telomeres protect cell chromosomes from fusing together or rearranging as this one can lead to cancer. Majority of cancer cells activate their telomerase which is not activated in normal cells except in stem cells. This one however is active in cancer cells (Barnett, Toman, Fisher, Long, 2004). expression profiling and proteomics have been tapped to transform the entire treatment and management of prostate cancer it helps in identifying new markers for screening, diagnosis, monitoring and execution of this therapy against this problem that affects majority of elderly men . Expression profiling has shown that the higher percentage of prostate cancers contain integration of genes resulting in the up regulation of ETS family transcription factors. The new diagnostic markers aimed at replacing PSA are being actively sought using a wide range of proteomic platforms (Boudjlida, 2000). Nevertheless, no single molecular marker has been discovered that is any more reliable for predicting outcome than histopathological grading. It is anticipated that in the future a small custom-built chips will be used to detect a minute panels of RNA or ascertain protein markers to answer certain questions that pertains patient management for each type of cancer. Conclusion Based on the above insight into the essence of transcriptomics and the relations in the process of comprehending, diagnosis, and treatment of cancer it clearly depicts the significance the field have and has contributed in saving human lives The convenience in the understanding of gene expression has greatly enabled oncologists in dealing with this problem which is inflicting many people in the societies nowadays. Transcriptomics has done medical and social good, therefore universities, medical schools, and medical training facilities should take with high regard this field by availing sufficient resources to teach students and equip researchers. Read More