17.06.02
Lecture 4 - Transcriptomics
* How can we distinguish 5' or 3' in UTR (untranslated region)?
- As using Markov chain model, we can predict 5' and 3' by focusing on their relationship.
- If we have reference, we can also predict 5' of UTR.
** What is Markov chain? **
- Markov chain refers to the sequence of random variables such a process moves through, with the Markov property defining serial dependence only between adjacent preiods.
- It can thus be used for describing systems that follow a chain of linked events, where what happens next depends only on the current state of the system.
* How can we distinguish whether it is UTR or not?
Score __________---------____________----------____________
5'UTR 5'UTR -> prediction
- Based on score which is checked by similarity, we can predict UTR.
* Expression is the ups and downs of gene products.
- Expression study ▶ Functional genomics, proteomics ▶ DNA chips, microaray, RNA-seq
* What is RNA?
- RNA is the first machineries of biochemistry of life.
- There are 10 millions of RNA in single cell. (Various structure, size, half life)
- RNA world : starting point of life.
- Transcription : make copy, reflection, one to one
- Translation : make complete different one, not one to one (triplet codon ▶ one amino acid)
- RNA vs. DNA
▶ RNA is unstable. DNA is stable.
▶ Number of oxyzen is different.
▶ Stable RNA exists during long period and makes many protein (prefer).
- RNA database
▶ RFAM (using hidden Markov model, 1 hidden Markov model represents all changes existed in one RNA species, RFAM is database stacking HMMs)
* One gene
- It has 7-8 exons.
- It can make various mRNA by RNA splicing process (exon skip, loss). ▶ 'Alternative splicing transcription'
- How many alternative splicing per gene? <10
* Microarray
1. Extract RNA and make cDNA with probe.
2. Make cDNA array which are consisted of knwon sequences.
3. Binding cDNA which is interested to cDNA array and check expression level.
▶ limit : we use knwon cDNA when we make array.
▶ normal vs. disease
* RNA sequencing
1. Extract RNA and make cDNA.
2. Sequencing cDNA.
+ Whole transcriptome analysis of six throughbred horses before and after exercise using RNA-seq to find difference between fast horse and slow horse.
▶ Alternative splicing which is occurred immediately of specific mRNA affects to this difference of velocity.
