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<p>Transcriptomics class for UNIST 20161. What is transcriptomics?</p>
<pul> <strongli>1. What is transcriptomics?study of transcriptome--> the complete set of RNA transcripts produced by DNA </strongli></pul>
<p> The study of <em>transcriptomics</em>, 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. </p>
<p><strong>2. Relationship between genomics and transcriptomics</strong> </p>
<p>Genomics is the study of genomes, thet total genes in cell or organisms2.Relationship between genomics and transcriptomics</p>
<pul>Transcriptomcs is the study <li>comparison of transcriptomes, allow the set identification of what kinds of all messenger RNA molecules genes are used in one certain cell or a population of cells. </pli></ul>
<p>I think genomics is a larger field or study than transcriptomics. This is because the transcriptomes are based on gene. </p>
<p><strong>3. What are mRNAs?</strong> </p>
<p> 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 expression3. Following transcription of primary transcript mRNA (known as pre mRNA) by RNA polymerase, processed, mature mRNA is translatedWhat are mRNAs? into a polymer of amino acids: a protein, as summarized in the central dogma of molecular biology.</p>
<pul> <strongli>4. How large family of RNA that convey genetic information from DNA to the ribosome</li> <li>related to measure transcription in which RNA expression?polymerase makes mRNA transcripts from template DNA</li> <li>processing </li> <li> <ul> <li>5' cap addition : critical for recognition by the ribosome / protection from RNases</li> <li>Editing : change nucleotide composition of the mRNA</li> <li>polyadenylation : protecting mRNA from degrading by exonucleases</li> </ul> </li> <li>structure</li> <li> <ul> <li>coding region : composed of codons, containing genetic information<br /> coding region begin with start codon and end with stop codon</li> <li>untranslated region ( 5' UTR / 3' UTR )</li> <li> <ul> <li>location : before the start codon / after the stop codon</li> <li>feature : locus which are not translated</li> <li>advantage : mRNA stability, mRNA localization , translational efficiency</li> </ul> </li> <li>poly(A) tail </li> <li> <ul> <li>composition : lone repetitive sequences of adenine nucleotides</li> <li>function : promote export from the nucleus / stimulate translation / protect the mRNA from degradation (by exonucleases)</li> </ul> </li> </ul> </strongli></pul>
<p>To measure the RNA expression, qPCR can be used <img src="file:///C:/Users/john/AppData/Local/Temp/enhtmlclip/search.jpg" /></p>
<p>qPCR is quantitative PCR. This is prevalently and widely used in laboratory. </p>
<p><strong>5. Relationship between Transcriptome and Proteome.</strong> </p>
<p>The proteome is the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time4. Proteome comes from transcriptome. In the central dogma, How to measure RNA expression?</p>
<pul>protein is the last step. DNA <li>high-throughput methods > mRNA : transcription , RNA -> protein : translationmicroarray</li></pul>
<p><strong>6. What is a UTR?</strong> </p>
<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>
<p><strong>75. Relationship between Transcriptome and Proteome. What is ncRNA ?</strong></p>
<pul>A non-coding RNA ( <emli>ncRNA</em>) transcriptome is an RNA molecule that related to the mRNA transcript while Proteome is not translated into a related to proteinproduct.Because mRNA is intermediate of protein production, there relative amount of expression can indicate the expression degrees of others.</li></pul>
<p>Non-coding RNA genes include highly abundant and functionally important RNAs such as transfer RNAs (tRNAs) and ribosomal RNAs(rRNAs), as well as RNAs such as microRNAs, siRNAs.</p> <p><strong>8. What is poly A ?</strong></p> <p>As its name it is, there are several As. To make this Poly A, there is needed polyadenylation. [[Polyadenylation]] is the addition of a <strong>poly(A) tail</strong> 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 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>
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<p>6. What to do:is a UTR?</p>
<pul>1. Apply <li>untranslated region ( 5' UTR / 3' UTR )</li> <li> <ul> <a href="httpli>location :before the start codon / after the stop codon</li> <li>feature : locus which are not translated</biolecture.orgli> <li>advantage : mRNA stability, mRNA localization , translational efficiency</index.phpli> </Biology_learning_procedure" title="Biology learning procedure"ul>Biology learning procedure </ali></pul>
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<p>Reference7. What is ncRNA ?</p>
<pul> <li>non-coding RNA : RNA molecule that is not translated into a href="http:protein</li> <li>function</www.biomedcentral.comli> <li> <ul> <li>gene-regulation</1471li> <li> <ul> <li>trans-2164acting ncRNAs : microRNAs</13/473"li> <li>httpcis-acting ncRNAs :riboswitch (5'-UTR)</li> </www.biomedcentral.comul> </1471-2164li> </13/473ul> </ali></pul>
<p>https://www.youtube.com/watch?v=UYJfM2-Y7y8 (Youtube by Illumina Gary Schroth)</p>
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<p>8. What is poly A ?</p>
<ul>
<li>composition : lone repetitive sequences of adenine nucleotides</li>
<li>function : promote export from the nucleus / stimulate translation / protect the mRNA from degradation (by exonucleases)</li>
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