View source for 17.06.02

<p><strong>Lecture 4&nbsp;- Transcriptomics</strong></p>

<p>* How can we distinguish 5&#39; or 3&#39; in UTR (untranslated region)?<br />
&nbsp;&nbsp;- As using&nbsp;Markov chain model, we can predict 5&#39; and 3&#39; by focusing on their relationship.<br />
&nbsp;&nbsp;- If we have reference, we can also predict 5&#39; of UTR.</p>

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<p>** What is Markov chain? **<br />
&nbsp;- 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.<br />
&nbsp;-&nbsp;It can thus be used for describing systems that follow a chain of linked events, where <u>what happens next depends only on the current state of the system</u>.</p>

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<p>* How can we distinguish whether it is UTR or not?</p>

<p>Score __________---------____________----------____________<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 5&#39;UTR &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;5&#39;UTR &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; -&gt; prediction</p>

<p>&nbsp;- Based on score which is checked by similarity, we can predict UTR.</p>

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<p>* Expression is the ups and downs of gene products.<br />
&nbsp;&nbsp;- Expression study&nbsp;▶ Functional genomics, proteomics&nbsp;▶ DNA chips, microaray, RNA-seq</p>

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<p>* What is RNA?<br />
&nbsp;&nbsp;- RNA is the first machineries of biochemistry of life.<br />
&nbsp;&nbsp;- There are&nbsp;10 millions of RNA in single cell. (Various structure, size, half life)&nbsp;<br />
&nbsp; - RNA world : starting point of life.</p>

<p>&nbsp; - Transcription : make copy, reflection, one to one<br />
&nbsp;&nbsp;- Translation : make complete different one, not one to one (triplet codon ▶&nbsp;one amino acid)<br />
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&nbsp;&nbsp;- RNA vs. DNA<br />
&nbsp; &nbsp;&nbsp;▶ RNA is unstable. DNA is stable.<br />
&nbsp; &nbsp;&nbsp;▶ Number of oxyzen is different.<br />
&nbsp;&nbsp; &nbsp;▶ Stable RNA exists during long period and makes many protein (prefer).<br />
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&nbsp;&nbsp;- RNA database<br />
&nbsp;&nbsp; &nbsp;▶ RFAM (using hidden Markov model, 1 hidden Markov model represents all changes existed in one RNA species, RFAM is database stacking HMMs)</p>

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<p>* One gene<br />
&nbsp;&nbsp;- It has 7-8 exons.<br />
&nbsp;&nbsp;- It can make various mRNA by RNA splicing process (exon skip, loss).&nbsp;▶ &#39;Alternative splicing transcription&#39;<br />
&nbsp; - How many alternative splicing per gene? &lt;10</p>

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<p>* Microarray<br />
&nbsp;&nbsp;1. Extract RNA and make cDNA with probe.<br />
&nbsp;&nbsp;2. Make cDNA array which are consisted of&nbsp;knwon sequences.<br />
&nbsp;&nbsp;3. Binding cDNA which is interested to cDNA array and check expression level.<br />
&nbsp; &nbsp; ▶ limit : we use knwon cDNA when we make array.<br />
&nbsp;&nbsp; &nbsp;▶ normal vs. disease</p>

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<p>* RNA sequencing<br />
&nbsp;&nbsp;1. Extract RNA and make cDNA.<br />
&nbsp;&nbsp;2. Sequencing cDNA.</p>

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<p>+ Whole transcriptome analysis of six throughbred horses before and after exercise using RNA-seq to find difference between fast horse and slow horse.<br />
&nbsp;&nbsp;▶ Alternative splicing which is occurred immediately of specific mRNA affects to this difference of velocity.</p>