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What Is Transcriptomics?
Transcriptomics is defined as the analysis of mRNA and non-coding RNAs that are in a cell at a given time. This is is “transcripts” of the genes that are being expressed in the cell. [1] It can be used to figure out the location of gene transcripts and when and if they are expressed in various cell types, as well as establishing levels of gene expression. Using that information, seeing how that changes in diseased cell can point to information on disease manifestation. [2] Depending on what is being analyzed, different tools can be used including RNA-seq, microarray, and qt-PCR. [1]
Techniques for Transcriptomics [1]
MicroarrayThis technique uses the transcriptomes that have a fluorescents attached and washes them over the array so that they bind to a complementary sequence. The color that shows up on an array indicates gene expression levels.
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RNA-seqThis technique uses the RNA from the cell, uses reverse transcription, and then sequenced. This will establish levels of gene expression, based on how many bind.
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Transcriptomics Results for DBT
Interacting Protein GRPEL2
Discussion
The report of RNA and protein analysis of DBT confirms that it is involved in metabolism as the protein is highly expressed in the pancreas, GI tract, urinary system, and endocrine tissues. An important finding is the comparison of transcript levels for DBT and its interacting protein, GRPEL2 (Figure 2). It is highly expressed in the esophagus, which leads to question of if the function of the esophagus is affecting feeding. In experiments, esophageal tissue can be assayed to determine if this is the case.
Another surprising find is in the expression level in the liver. It has higher RNA levels, but fairly average protein levels. A treatment for MSUD is a liver transplant [4]. Based on this, it would be thought that the protein is highly expressed in these tissues (in comparison to other tissues). This is a potential area for future research as to why the transplant rescues the phenotype, even though that is not the tissue of highest expression. This information could also be used to research whether or not a kidney transplant could also rescue the phenotype since it expresses DBT RNA and protein at such high levels.
Another surprising find is in the expression level in the liver. It has higher RNA levels, but fairly average protein levels. A treatment for MSUD is a liver transplant [4]. Based on this, it would be thought that the protein is highly expressed in these tissues (in comparison to other tissues). This is a potential area for future research as to why the transplant rescues the phenotype, even though that is not the tissue of highest expression. This information could also be used to research whether or not a kidney transplant could also rescue the phenotype since it expresses DBT RNA and protein at such high levels.
References:
[1] Blackburn, L., (August 2017). What is transcriptomics. Retrieved from: http://www.phgfoundation.org/blog/what-is-transcriptomics
[2] NIH. (August 2015). Transcriptome. Retrieved from: https://www.genome.gov/13014330/transcriptome-fact-sheet/
Human Protein Atlas. (n.d.) DBT. Retrieved from https://www.proteinatlas.org/ENSG00000137992-DBT/tissue
[3] https://www.ncbi.nlm.nih.gov/gene/134266
[4] Strauss, K., Puffenberger, E., Morton, H. (May 2013). Maple Syrup Urine Disease. Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK1319/#msud.molgen.TA
Images:
Header: 521594890_1280x720.jpg
All other images are linked
[1] Blackburn, L., (August 2017). What is transcriptomics. Retrieved from: http://www.phgfoundation.org/blog/what-is-transcriptomics
[2] NIH. (August 2015). Transcriptome. Retrieved from: https://www.genome.gov/13014330/transcriptome-fact-sheet/
Human Protein Atlas. (n.d.) DBT. Retrieved from https://www.proteinatlas.org/ENSG00000137992-DBT/tissue
[3] https://www.ncbi.nlm.nih.gov/gene/134266
[4] Strauss, K., Puffenberger, E., Morton, H. (May 2013). Maple Syrup Urine Disease. Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK1319/#msud.molgen.TA
Images:
Header: 521594890_1280x720.jpg
All other images are linked