Expressomics

Expressomics is the analysis of the transcripts of RNA produced by the genotype at a given time. It is able to provide a link between the genome, the proteome, and the cellular phenotype.[1] Expressomics is a relatively new term and many researchers know it as transcriptomics or gene sequence analysis. Expressomics is a whole genome-based approach in genomics.[2] With the development of the Next-Generation sequencing technologies, the field of expressomics has developed quickly.[3]

Techniques

There are three basic techniques to analyze the expressome: DNA Microarray, RNA-seq, and Real-time PCR.[4][5]

DNA Microarray

This is a technique that has been in use for many years. These are chips that have thousands of tiny DNA spots marked on them, where each spot represents a gene of interest. This technique has limits to the number of genes that it can hold.[3]

RNA-Seq

This is the most recent technique of expressomics. This method will probably replace microarray completely in the next 5–10 years. This technology allows researchers to sequence huge amounts of DNA or RNA in a short amount of time. You could sequence millions of mRNA strands and output them into a computer file in a matter of hours. These types of sequencing technologies are called next-generation or deep-sequencing methods. The RNA-seq method has the potential to provide information on gene expression in every gene, or close to every gene.[6]

Real-Time PCR

Real-time PCR has been shown to be more efficient, sensitive, and reliable than other gene expression techniques. It is used to amplify and quantify a targeted DNA molecule. The accuracy and reliability of this technique is dependent upon the choice of appropriate reference genes.[5] This method uses PCR and fluorescence to measure gene expression.[7]

Applications and Research

Expressomics has grown quickly in medicine and pharmaceuticals, biotechnology, agrochemical industries, and food industries.[8] These are two examples of expressomic technologies being used in research.

Digestive Enzymes in Pacific White Shrimp

The Pacific White Shrimp, Litopenaeus vannamei, go through metamorphosis. It consists of five stages in early development known as: embryo, nauplius, zoea, mysis, and postlarvae. The researchers determined that the diet of the shrimp changes through each step of development and they wanted to see if there was a difference in the enzymes that are present during each developmental stage. They used RNA-seq data to analyze the types and expression characteristics of the digestive enzymes genes during all five stages of development. The results showed that sixteen different digestive enzymes were present during the five stages. There were five types of carbohydrase enzymes, seven types of pepsidase enzymes, and four types of lipase enzymes. They found that the carbohydrases, pepsidases, and lipases were more heavily expressed during the final three stages of development. The diverse set of enzymes shows how L. vannamei can have varied diets to fit the nutritional requirements at different points in development. These results provide support to better understand the physiological changes that happen during the transitions between developmental stages.[9]

LincRNAs in Breast Cancer

In this study, the researchers wanted to find the correlation of the expression of long intergenic noncoding RNAs (lincRNAs) in cancer. Twenty-five samples of breast cancer tissue and normal tissue located near the cancer tissue were taken and studied for the expression of lincRNAs by RNA-seq. There were 538 lincRNAs studies and 124 lincRNAs were solely expressed in the cancer adjacent tissues and 62 lincRNAs were solely expressed in the breast cancer tissues. They also found that the expression of 134 lincRNAs was higher in the breast cancer tissue and 272 were lower in comparison with the normal tissue. Four selected lincsRNAs (BC2, BC4, BC5, and BC8) were analyzed by semi-quantitative and real-time PCR. This showed that the expression of lincRNA-BC5 was positively correlated with patients’ age, pathological stage, and progesterone receptor concentration.[10] The lincRNA-BC8 was negatively correlated with progesterone receptor expression. LincRNA-BC4 was seen in the advanced stages of breast cancer and lincRNA-BC2 showed no specific changes in the pathological features that were studied. These results show that these lincRNAs are expressed differently in breast cancer. This outcome suggests that they might have prominent roles in the function of oncogenes or tumor suppressors that affect the development of breast cancer.[10]

References

  1. ↑ Cocolin, Luca, and Kalliopi Rantsiou. "Molecular Biology- Transcriptomics." Encyclopedia of Food Microbiology Second Edition (2014): 803-07. Print.
  2. ↑ Binder, Elizabeth, and Charles Nemeroff. "Implications for the Practice of Psychiatry." Functional Genomics and Proteomics in the Clinical Neurosciences. Vol. 158. Amsterdam: Elsevier, 2006. 275-276. Print.
  3. 1 2 McGettigan, Paul A (2013). "Transcriptomics in the RNA-seq Era". Current Opinion in Chemical Biology 17 (1): 4–11. doi:10.1016/j.cbpa.2012.12.008.
  4. ↑ Lui, Edmund; Long, Yan; Lin Tan, Tuan; Timms, Peter; Marie Hafner, Louise; et al. (2014). "Elucidating the Host–pathogen Interaction between Human Colorectal Cells and Invading Enterovirus 71 Using Transcriptomics Profiling". FEBS Open Bio 4: 426–31. doi:10.1016/j.fob.2014.04.005.
  5. 1 2 Gong et al. "Identification and Validation of Suitable Reference Genes for RT‑qPCR Analysis in Mouse Testis Development." Molecular Genetics and Genomics (2014). Web. 30 Oct. 2014.
  6. ↑ Wang, Zhong, Mark Gerstein, and Michael Snyder. "RNA-Seq: A Revolutionary Tool for Transcriptomics." Nature Reviews Genetics 10.1 (2009): 57-63. Print.
  7. ↑ Safdar, M., and M.F. Abasiyanik. "Development of Fast Multiplex Real-time PCR Assays Based on EvaGreen Fluorescence Dye for Identification of Beef and Soybean Origins in Processed Sausages." Food Research International 54.2 (2013): 1652-656. Science Direct. Web. 3 Nov. 2014. <http://ejournals.ebsco.com.libdata.lib.ua.edu/Direct.asp?AccessToken=7TTTOT3B3MRIM0XONIITX3ODRO9MBT33D3&Show=Object>.
  8. ↑ Sarmah, Chintanu Kumar, and Sandhya Samarasinghe. "An Approach To Compare Affymetrix And Cdna Gene Expressions." Current Science (00113891) 102.11 (2012): 1565-1570. Academic Search Premier. Web. 16 Nov. 2014.
  9. ↑ Wei, Jiankai, Xiaojun Zhang, Yang Yu, Fuhua Li, and Jianhai Xiang. "RNA-Seq Reveals the Dynamic and Diverse Features of Digestive Enzymes during Early Development of Pacific White Shrimp Litopenaeus Vannamei."Comparative Biochemistry and Physiology Part D: Genomics and Proteomics11 (2014): 37-44.Science Direct. Web. 28 Sept. 2014. <http://www.sciencedirect.com/science/article/pii/S1744117X14000331>. .
  10. 1 2 Ding, Xianfeng, et al. "Long Intergenic Non-Coding Rnas (Lincrnas) Identified By RNA-Seq In Breast Cancer." Plos ONE 9.8 (2014): 1-10. Academic Search Premier. Web. 16 Nov. 2014.

External links

See also

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