Difference between revisions of "Transcriptomics"

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imported>Jiyoung Oh
imported>S
 
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<p>Transcriptomics&nbsp;class for UNIST 2016</p>
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<p>1. What is transcriptomics?</p>
  
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<p><strong>1. What is transcriptomics?</strong></p>
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<ul>
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<li>study of transcriptome--&gt; the complete set of RNA transcripts produced by DNA&nbsp;</li>
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<li>The&nbsp;transcriptome&nbsp;is the set of all messenger RNA (mRNA)&nbsp;molecules in one cell or a population of cells.&nbsp;It differs from the exome&nbsp;in that it includes only those RNA molecules found in a specified cell population, and usually includes the amount or concentration of each RNA molecule in addition to the molecular identities.</li>
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</ul>
  
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<p>&nbsp;The study of&nbsp;<em>transcriptomics</em>, also referred to as expression profiling,&nbsp;examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA microarray&nbsp;technology.&nbsp;</p>
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<p>&nbsp; - measuring : micro array and RNA-seq are used for measure about transcriptome in organisms.</p>
  
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<p><strong>2. Relationship between genomics and transcriptomics</strong></p>
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<p>&nbsp;</p>
  
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<p>Genomics is the study of genomes, thet total genes in cell or organisms.</p>
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<p>2. Relationship between genomics and transcriptomics</p>
  
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<p>Transcriptomcs is the study of transcriptomes,&nbsp;the set of all messenger RNA molecules in one cell or a population of cells.&nbsp;</p>
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<ul>
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<li>comparison of transcriptomes allow the identification of what kinds of genes are used in certain cell</li>
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</ul>
  
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<p>I think genomics is a larger field or study than transcriptomics. This is because the transcriptomes are based on gene.</p>
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<p>&nbsp;</p>
  
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<p><strong>3. What are mRNAs?</strong></p>
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<p>&nbsp;</p>
  
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<p>&nbsp;This is called messenger RNA.&nbsp;&nbsp;mRNA is a large family of RNA&nbsp;molecules that convey genetic information&nbsp;from DNA to the ribosome,&nbsp;where they specify the amino acid&nbsp;sequence of the protein&nbsp;products of gene expression. Following transcription of primary transcript&nbsp;mRNA (known as pre mRNA)&nbsp;by RNA polymerase, processed, mature mRNA is translated&nbsp;into a polymer of amino acids: a protein, as summarized in the central dogma of molecular biology.</p>
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<p>3. What are mRNAs?&nbsp;</p>
  
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<p><strong>4. How to measure RNA expression?</strong></p>
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<ul>
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<li>large family of RNA that convey genetic information from DNA to the ribosome</li>
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<li>related to transcription in which RNA polymerase makes mRNA transcripts from template DNA</li>
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<li>processing&nbsp;</li>
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<li>
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<ul>
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<li>5&#39; cap addition : critical for recognition by the ribosome &nbsp;/ protection from RNases</li>
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<li>Editing : change nucleotide composition of the mRNA</li>
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<li>polyadenylation : protecting mRNA from degrading by exonucleases</li>
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</ul>
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</li>
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<li>structure</li>
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<li>
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<ul>
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<li>coding region : composed of codons, containing genetic information<br />
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&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;coding region begin with start codon and end with stop codon</li>
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<li>untranslated region ( 5&#39; UTR / 3&#39; UTR&nbsp;)</li>
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<li>
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<ul>
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<li>location : before the start codon &nbsp;/ after the stop codon</li>
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<li>feature : locus which are not translated</li>
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<li>advantage : mRNA stability, mRNA localization , translational efficiency</li>
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</ul>
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</li>
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<li>poly(A) tail&nbsp;</li>
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<li>
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<ul>
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<li>composition : lone repetitive sequences of adenine nucleotides</li>
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<li>function : promote export from the nucleus / stimulate translation / protect the mRNA from degradation (by exonucleases)</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
  
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<p>To measure the RNA expression, qPCR can be used.</p>
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<p>&nbsp; &nbsp; &nbsp;<img src="file:///C:/Users/john/AppData/Local/Temp/enhtmlclip/search.jpg" /></p>
  
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<p>qPCR is quantitative PCR. This is prevalently and widely used in laboratory.</p>
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<p>&nbsp;</p>
  
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<p><strong>5. Relationship between Transcriptome and Proteome.</strong></p>
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<p>&nbsp;</p>
  
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<p>The proteome&nbsp;is the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time. Proteome comes from transcriptome. In the central dogma,&nbsp;</p>
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<p>4. How to measure RNA expression?</p>
  
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<p>protein is the last step. DNA -&gt; mRNA : transcription , RNA -&gt; protein : translation</p>
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<ul>
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<li>high-throughput methods &gt;&gt; microarray</li>
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</ul>
  
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<p><strong>6. What is a UTR?</strong></p>
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<p>&nbsp;</p>
  
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<p>In molecular genetics, an untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA.</p>
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<p>&nbsp;</p>
  
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<p><strong>7. What is ncRNA&nbsp;?</strong></p>
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<p>5. Relationship between Transcriptome and Proteome.</p>
  
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<p>A non-coding RNA (<em>ncRNA</em>) is an RNA molecule that is not translated into a protein.</p>
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<ul>
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<li>transcriptome is related to the mRNA transcript while Proteome is related to protein product. Because mRNA is intermediate of protein production, there relative amount of expression can indicate the expression degrees of others.</li>
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</ul>
  
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<p>Non-coding RNA genes include highly abundant and functionally important RNAs such as transfer RNAs&nbsp;(tRNAs) and ribosomal RNAs(rRNAs), as well as RNAs such as microRNAs, siRNAs.</p>
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<p>&nbsp;</p>
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<p><strong>8. What is poly A&nbsp;?</strong></p>
 
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<p>As its name it is, there are several As. To make this Poly A, there is needed polyadenylation. [[Polyadenylation]]&nbsp;is the addition of a&nbsp;<strong>poly(A) tail</strong>&nbsp;to a mRNA. The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine&nbsp;bases. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation. It, therefore, forms part of the larger process of gene expression.</p>
 
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>What to do:</p>
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<p>6. What is a UTR?</p>
  
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<p>1. Apply&nbsp;<a href="http://biolecture.org/index.php/Biology_learning_procedure" title="Biology learning procedure">Biology learning procedure</a></p>
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<ul>
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<li>untranslated region ( 5&#39; UTR / 3&#39; UTR&nbsp;)</li>
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<li>
 +
<ul>
 +
<li>location : before the start codon &nbsp;/ after the stop codon</li>
 +
<li>feature : locus which are not translated</li>
 +
<li>advantage : mRNA stability, mRNA localization , translational efficiency</li>
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</ul>
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</li>
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</ul>
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>Reference</p>
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<p>7. What is ncRNA&nbsp;?</p>
  
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<p><a href="http://www.biomedcentral.com/1471-2164/13/473">http://www.biomedcentral.com/1471-2164/13/473</a></p>
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<ul>
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<li>non-coding RNA : RNA molecule that is not translated into a protein</li>
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<li>function</li>
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<li>
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<ul>
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<li>gene-regulation</li>
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<li>
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<ul>
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<li>trans-acting ncRNAs : microRNAs</li>
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<li>cis-acting ncRNAs : riboswitch (5&#39;-UTR)</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
  
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<p>https://www.youtube.com/watch?v=UYJfM2-Y7y8 &nbsp;(Youtube by Illumina Gary Schroth)</p>
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<p>&nbsp;</p>
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<p>8. What is poly A&nbsp;?</p>
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 +
<ul>
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<li>composition : lone repetitive sequences of adenine nucleotides</li>
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<li>function : promote export from the nucleus / stimulate translation / protect the mRNA from degradation (by exonucleases)</li>
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</ul>

Latest revision as of 20:27, 1 December 2016

1. What is transcriptomics?

  • study of transcriptome--> the complete set of RNA transcripts produced by DNA 
  • The transcriptome is the set of all messenger RNA (mRNA) molecules in one cell or a population of cells. It differs from the exome in that it includes only those RNA molecules found in a specified cell population, and usually includes the amount or concentration of each RNA molecule in addition to the molecular identities.

  - measuring : micro array and RNA-seq are used for measure about transcriptome in organisms.

 

2. Relationship between genomics and transcriptomics

  • comparison of transcriptomes allow the identification of what kinds of genes are used in certain cell

 

 

3. What are mRNAs? 

  • large family of RNA that convey genetic information from DNA to the ribosome
  • related to transcription in which RNA polymerase makes mRNA transcripts from template DNA
  • processing 
    • 5' cap addition : critical for recognition by the ribosome  / protection from RNases
    • Editing : change nucleotide composition of the mRNA
    • polyadenylation : protecting mRNA from degrading by exonucleases
  • structure
    • coding region : composed of codons, containing genetic information
                             coding region begin with start codon and end with stop codon
    • untranslated region ( 5' UTR / 3' UTR )
      • location : before the start codon  / after the stop codon
      • feature : locus which are not translated
      • advantage : mRNA stability, mRNA localization , translational efficiency
    • poly(A) tail 
      • composition : lone repetitive sequences of adenine nucleotides
      • function : promote export from the nucleus / stimulate translation / protect the mRNA from degradation (by exonucleases)

     

 

 

4. How to measure RNA expression?

  • high-throughput methods >> microarray

 

 

5. Relationship between Transcriptome and Proteome.

  • transcriptome is related to the mRNA transcript while Proteome is related to protein product. Because mRNA is intermediate of protein production, there relative amount of expression can indicate the expression degrees of others.

 

 

6. What is a UTR?

  • untranslated region ( 5' UTR / 3' UTR )
    • location : before the start codon  / after the stop codon
    • feature : locus which are not translated
    • advantage : mRNA stability, mRNA localization , translational efficiency

 

 

7. What is ncRNA ?

  • non-coding RNA : RNA molecule that is not translated into a protein
  • function
    • gene-regulation
      • trans-acting ncRNAs : microRNAs
      • cis-acting ncRNAs : riboswitch (5'-UTR)

 

 

8. What is poly A ?

  • composition : lone repetitive sequences of adenine nucleotides
  • function : promote export from the nucleus / stimulate translation / protect the mRNA from degradation (by exonucleases)
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