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5. Epigenomics and Proteomics Class (0610)

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<pstyle="margin-left: 40px"><strong>&nbsp; Epigenetics </strong>is the study of epigenetic variations which switch the gene expression by environment factor without affecting sequence of DNA. There are examples of epigenetic &nbsp; modification, DNA methylation, histone modification, and RNA interference.</p>
<hr p><strong>&nbsp;&nbsp;&nbsp; 1) DNA methylation</strong></p> <pstyle="margin-left: 40px">&nbsp;&nbsp;It is process which the methyl group is added to the DNA. When the promoter of gene is methylated, then it represses the gene expression. Adenine and cytosine can be methylated,&nbsp;adenine methylation occurs only in prokaryotes. DNA methyltransferase 1is an enzyme which transfer methyl group to DNA, and they work as tissue specific manner. DNA methylation has&nbsp; important roles in mammalian system. Genomic imprinting, X-chromosome inactivation, Heterochromatin maintenance, Developmental controls, Tissue specific expression controls.</p> <p style="margin-left: 40px">&nbsp;Genomic imprinting can be caused by DNA methylation, and histone methylation which is independent of Mendelian inheritance. Expression of gene is inherited from mother or father. X-chromosome inactivation is the process which one of the two X chromosomes in all female cells is inactivated. Females(XX) carry twice as many dosage of gene as males(XY), so in order to solve this problem one X chromosome is inactivated randomly by methylations in the early developmental process. Chromatin can be found as two status, heterochromatin and euchromatin. Heterochromatin is tightly packed form of DNA, and controlled by DNA methylation. As I mention above, DNMT1 act as tissue specific manner, so DNA methylationcan control gene expression tissue specific manner.</p> <p><strong>&nbsp;&nbsp; 2) Histone modification.</strong></p>
<pstyle="margin-left: 40px">&nbsp; It Basic unit of DNA packing is process nucleosome which the methyl group is added to the consists of DNAwound around eight histones protein. This histone octamer consists of two copies of H2A, H2B, H3, and H4. When In the promoter class, we think about why it consists of gene is methylatedfour different types, then not simply one type. Jong said that it represses the might be one type long time ago, but as we develop, more diverse regulation of gene expressionmight be needed. Adenine I agree with this and cytosine can I think that H2A and H2B might be methylated, adenine methylation occurs only in prokaryotes. DNA methyltransferase 1 is an enzyme which transfer methyl group to DNAone type before, and they work but as tissue specific manner. DNA methylation has important roles in mammalian system. Genomic imprintingwe need more regulation function, X-chromosome inactivation, Heterochromatin maintenance, Developmental controls, Tissue specific expression controlsit might be differentiated into two similar types recently.</p>
<pstyle="margin-left: 40px">&nbsp;Genomic imprinting Histone modification is modification to the histone proteins. Because role of histone protein is packing of DNA, modification of it alters gene expression by regulating packing. At tightly packed DNA, transcription factor can be caused by &rsquo;t easily bind to the DNA , so gene expression is down regulated. Modification includes methylation, phosphorylation, acetylation, ubiquitiylation, and sumoylation. It usually happens in the tail protruding from the histone core of the nucleosome, and also this modification site exits within the globular histone core. In the class, we think about why histone tail exists. I think that enzyme like DNMT1 can easily bind to the histone tail than histone methylation which core because histone tail is independent of Mendelian inheritancemore accessible than histone core. Expression I guess that that&rsquo;s why the modification of gene histone tail is inherited from mother or fathermore common than modification of histone core.</p>
<pstyle="margin-left: 40px">&nbsp;&nbsp;X-chromosome inactivation is the process which one of the two X chromosomes in all female cells is inactivated. Females(XX) carry twice as many dosage of gene as males(XY), so in order to solve this problem one X chromosome is inactivated randomly by methylations in the early developmental process in.</p>
<pstyle="margin-left: 40px">&nbsp;Chromatin can be found as two status, heterochromatin and euchromatinThere are many technologies for studying epigenomics. In the class I learned about bisulfate sequencing. Heterochromatin When bisulfate is tightly packed form of treated to the DNA, cytosine residues are converted to uracil, but 5-methylcytosine residues is not affected. By sequencing, we can know the methylated and controlled by DNA methylationunmethylated cytosine.</p>
<hr /><p><strong>&nbsp;&nbsp;&nbsp;As I mention above, DNMT1 act as tissue specific manner, so DNA methylation can control gene expression tissue specific manner.Proteomics </strong></p>
<p>&nbsp;</p>
 
<p><strong>&nbsp;&nbsp; 1) What is proteome?</strong></p>
 
<p style="margin-left: 40px">Proteome is the entire set of protein which expressed under the specific condition. Proteomics is the study of proteome. It study about interaction between proteins, and expression level of protein under the specific condition.</p>
 
<p><strong>&nbsp;&nbsp; 2) Relationship between genomics, transcriptomics, and proteomics.</strong></p>
 
<p style="margin-left: 40px">Protein is&nbsp;ultimate purpose of&nbsp;exsistance of genome and transcriptome, so study of proteome, proteomics is closely related to phenotype.</p>
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