Difference between revisions of "Transcriptomics"

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imported>Eunseok yoo
imported>Jiyoung Oh
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<h1><span style="font-size: medium;">Definition</span></h1>
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<p>Transcriptomics class for UNIST 2015</p>
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<p><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">The&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">transcriptome</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;is the set of all RNA molecules, including&nbsp;</span><a href="http://en.wikipedia.org/wiki/Messenger_RNA" title="Messenger RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">mRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">,&nbsp;</span><a href="http://en.wikipedia.org/wiki/Ribosomal_RNA" title="Ribosomal RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">rRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">,&nbsp;</span><a href="http://en.wikipedia.org/wiki/Transfer_RNA" title="Transfer RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">tRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, and other&nbsp;</span><a href="http://en.wikipedia.org/wiki/Non-coding_RNA" title="Non-coding RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">non-coding RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;</span><a href="http://en.wikipedia.org/wiki/Transcription_(genetics)" title="Transcription (genetics)" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">transcribed</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;in one cell or a population of&nbsp;</span><a href="http://en.wikipedia.org/wiki/Cell_(biology)" title="Cell (biology)" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">cells</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">.&nbsp;</span></p>
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<h1><span style="font-size: medium;">classification of RNA molecule</span></h1>
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<p>1. What is transcriptomics?</p>
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<h2><font size="3"><span style="font-size: medium;">mRNA</span></font></h2>
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<p><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">Messenger RNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">mRNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) is a large family of&nbsp;</span><a href="http://en.wikipedia.org/wiki/RNA" title="RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;molecules that convey&nbsp;</span><a href="http://en.wikipedia.org/wiki/Genetic_information" title="Genetic information" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">genetic information</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;from&nbsp;</span><a href="http://en.wikipedia.org/wiki/DNA" title="DNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">DNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;to the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Ribosome" title="Ribosome" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">ribosome</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, where they specify the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Amino_acid" title="Amino acid" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">amino acid</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">sequence of the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Protein" title="Protein" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">protein</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;products of&nbsp;</span><a href="http://en.wikipedia.org/wiki/Gene_expression" title="Gene expression" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">gene expression</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">. Following&nbsp;</span><a href="http://en.wikipedia.org/wiki/Transcription_(genetics)" title="Transcription (genetics)" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">transcription</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;of&nbsp;</span><a href="http://en.wikipedia.org/wiki/Primary_transcript" title="Primary transcript" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">primary transcript</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;mRNA (known as&nbsp;</span><a href="http://en.wikipedia.org/wiki/Precursor_mRNA" title="Precursor mRNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">pre-mRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) by&nbsp;</span><a href="http://en.wikipedia.org/wiki/RNA_polymerase" title="RNA polymerase" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA polymerase</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, processed, mature mRNA is&nbsp;</span><a href="http://en.wikipedia.org/wiki/Translation_(genetics)" title="Translation (genetics)" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">translated</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;into a polymer of amino acids</span></p>
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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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<h3 style="margin-left: 40px;"><span style="font-size: medium;">UTR</span></h3>
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<p style="margin-left: 40px;"><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">In&nbsp;</span><a href="http://en.wikipedia.org/wiki/Molecular_genetics" title="Molecular genetics" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">molecular genetics</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, an&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">untranslated region</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(or&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">UTR</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) refers to either of two sections, one on each side of a&nbsp;</span><a href="http://en.wikipedia.org/wiki/Coding_sequence" title="Coding sequence" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">coding sequence</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;on a strand of&nbsp;</span><a href="http://en.wikipedia.org/wiki/MRNA" title="MRNA" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">mRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">. If it is found on the 5' side, it is called the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Five_prime_untranslated_region" title="Five prime untranslated region" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">5' UTR</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(or&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">leader sequence</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">), or if it is found on the 3' side, it is called the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Three_prime_untranslated_region" title="Three prime untranslated region" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">3' UTR</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(or&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">trailer sequence</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">).</span></p>
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<p>2. Relationship between genomics and transcriptomics</p>
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<h3 style="margin-left: 40px;"><span style="font-size: medium;">poly A</span></h3>
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<p style="margin-left: 40px;"><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">Polyadenylation</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;is the addition of a&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">poly(A) tail</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;to a&nbsp;</span><a href="http://en.wikipedia.org/wiki/Messenger" title="Messenger" class="mw-disambig" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">messenger</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;</span><a href="http://en.wikipedia.org/wiki/RNA" title="RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">.&nbsp;</span><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">The poly(A) tail is important for the nuclear export, translation, and stability of mRNA. The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded.</span></p>
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<p>Genomics is the study of genomes, thet total genes in cell or organisms.</p>
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<h2><span style="font-size: medium;">ncRNA</span></h2>
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<p><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">A&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">non-coding RNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">ncRNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) is a functional&nbsp;</span><a href="http://en.wikipedia.org/wiki/RNA" title="RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;molecule that is not&nbsp;</span><a href="http://en.wikipedia.org/wiki/Translation_(genetics)" title="Translation (genetics)" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">translated</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;into a&nbsp;</span><a href="http://en.wikipedia.org/wiki/Protein" title="Protein" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">protein</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">.&nbsp;</span><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">Non-coding RNA genes include highly abundant and functionally important RNAs such as&nbsp;</span><a href="http://en.wikipedia.org/wiki/Transfer_RNA" title="Transfer RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">transfer RNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(tRNAs) and&nbsp;</span><a href="http://en.wikipedia.org/wiki/Ribosomal_RNA" title="Ribosomal RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">ribosomal RNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">(rRNAs), as well as RNAs such as&nbsp;</span><a href="http://en.wikipedia.org/wiki/MicroRNA" title="MicroRNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">microRNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">,&nbsp;</span><a href="http://en.wikipedia.org/wiki/SiRNA" title="SiRNA" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">siRNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">,&nbsp;and&nbsp;</span><a href="http://en.wikipedia.org/wiki/SnRNA" title="SnRNA" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">snRNAs</a>.</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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<h1><span style="font-size: medium;">measurment of RNA expression</span></h1>
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<p><a href="http://en.wikipedia.org/wiki/RNA-seq" title="RNA-seq" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA-seq</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;is emerging (2013) as the method of choice for measuring transcriptomes of organisms, though the older technique of&nbsp;</span><a href="http://en.wikipedia.org/wiki/DNA_microarray" title="DNA microarray" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">DNA microarrays</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;is still used.</span></p>
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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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<h1><span style="font-size: medium;">Relationship among genome, transcriptome, and proteome</span></h1>
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<p><img src="/ckfinder/userfiles/images/nature06802-f2_2.jpg" width="800" height="335" alt="" /></p>
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<p>3. What are mRNAs?</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>4. How to measure RNA expression?</p>
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<p>&nbsp;</p>
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<p>5. Relationship between Transcriptome and Proteome.</p>
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<p>6. What is a UTR?</p>
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<p>7. What is ncRNA&nbsp;?</p>
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<p>8. What is poly A&nbsp;?</p>
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<p>&nbsp;</p>
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<p>&nbsp;</p>
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<p>What to do:</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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<p>&nbsp;</p>
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<p>&nbsp;</p>
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<p>Reference</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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<p>https://www.youtube.com/watch?v=UYJfM2-Y7y8 &nbsp;(Youtube by Illumina Gary Schroth)</p>
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<p>&nbsp;</p>

Revision as of 14:54, 29 May 2016

Transcriptomics class for UNIST 2015

1. What is transcriptomics?

 The study of transcriptomics, also referred to as expression profiling, examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA microarray technology. 

2. Relationship between genomics and transcriptomics

Genomics is the study of genomes, thet total genes in cell or organisms.

Transcriptomcs is the study of transcriptomes, the set of all messenger RNA molecules in one cell or a population of cells. 

I think genomics is a larger field or study than transcriptomics. This is because the transcriptomes are based on gene.

3. What are mRNAs?

 This is called messenger RNA.  mRNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. Following transcription of primary transcript mRNA (known as pre mRNA) by RNA polymerase, processed, mature mRNA is translated into a polymer of amino acids: a protein, as summarized in the central dogma of molecular biology.

4. How to measure RNA expression?

 

5. Relationship between Transcriptome and Proteome.

6. What is a UTR?

7. What is ncRNA ?

8. What is poly A ?

 

 

What to do:

1. Apply Biology learning procedure

 

 

Reference

http://www.biomedcentral.com/1471-2164/13/473

https://www.youtube.com/watch?v=UYJfM2-Y7y8  (Youtube by Illumina Gary Schroth)

 

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