4. Transcriptomics Class (0603)
What is transcriptomics?
Transcriptomics is study of transcriptome which is the total messenger RNA within a cell or organism.
Relationship between genomics and transcriptomics
Genomics is study of total DNA of cell or organism. Genetic information is encoded in the DNA, and the some portion of DNA is transcribed to mRNA when it is needed. Therefore, transcriptomics give some information of gene expression. From the same genetic information, transcription can be regulated due to different cell type and cellular environment. I think that it is important because it is the first step to show the phenotype difference from the same genetic information.
What are mRNAs?
RNA is classified into two categories, coding RNA and non coding RNA. Messenger RNA is included in the coding RNA. It means that they encode amino acid sequences, so they act as template for protein synthesis. It consists of 5’ cap, 5’ UTR, coding sequence, 3’ UTR, Poly-A tail.
How to measure mRNA expression?
I learned from the lecture, and among them I searched about RNA-seq and microarray. RNA-seq is deep-sequencing technologies. First ome portion or total RNA is extracted from the cell, and they are converted to the cDNA. They are sequenced in a high-throughput manner by using Illumina IG, Applied Biosystem SOLiD, and so on, so this is expensive. Microarray is used to measure expression level of some genes, and for genotyping. At the solid surface, probe which is short sequence of RNA is anchored, and the RNA which have complementary to the probe is hybridized with the probe. Then, it is quantified by using fluoroscent. So, microarray only measure the expression of gene which is complementary to the probe. It can't detect novel transcripts, gene fusion, but RNA-seq can do this. Also, RNA-seq is more sensitive and specific.
Relationship between transcriptome and proteome.
As I mentioned before, protein is made from the transcribed mRNA. The final aim of mRNA is to produce protein which changes phenotype, so I think that study of proteome is more efficient way to measure gene expression than study of transcriptome. Half life of RNA is short because it can be easily degraded by environmental change like temperature or pH. As a result, amount of protein is usually not correlated to amount of mRNA.
What is a UTR?
It is untranslated region in the mRNA. There are two UTR, one exists before the start codon, 5’ UTR, and the other exists after the start codon, 3’ UTR. They have roles in the mRNA stability, mRNA localization, and translational efficiency. mRNA stability is controlled by RNA degrading enzyme which is controlled by UTR. UTR have some information about localization of mRNA. Also, UTR regulate translation efficiency by affecting the ribosome binding to the mRNA.
What is ncRNA?
ncRNA is non-coding RNA, and it is RNA which is not coding amino acid. It include tRNAs, snoRNAs, rRNAs, microRNAs, siRNAs, snRNAs, exRNAs, piRNAs and scaRNAs.
What is poly A?
It is portion of mRNA which consist of long sequence of adenine nucleotides in the 3’ end of the mRNA. It promotes export from nucleus and translation, and protect the mRNA from degradation.