Difference between revisions of "Histone Deacetylase (Katie Richeson)"
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In completing a blastn search for this [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?exportGenes=1&exportType=nucleic&gene_oid=644029844&up_stream=0&down_stream=0 gene sequence] I found many different hits from other halophiles but none of the hits described any sort of function. The results only showed that this sequence is often found in other halophiles, such as [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=AB73GBC601N&log%24=nucltop&blast_rank=2&list_uids=55229667 Haloarcula marismortui]. | In completing a blastn search for this [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?exportGenes=1&exportType=nucleic&gene_oid=644029844&up_stream=0&down_stream=0 gene sequence] I found many different hits from other halophiles but none of the hits described any sort of function. The results only showed that this sequence is often found in other halophiles, such as [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=AB73GBC601N&log%24=nucltop&blast_rank=2&list_uids=55229667 Haloarcula marismortui]. | ||
| − | I next went on the compare the sequence to halophile genomes that have already been annotated in order to determine if the function of similar sequences was the same. I started with Haloferax volcanii using the GeneBank annotation data and found 1 histone deacetylase gene and 3 histone acetylases. I think it is important to note that while searching the list of functional genes for our species I found no acetyltransferase genes, which asks the question. . . What is placing the acetyl groups on the histone that the deacetylase is removing OR is the deacetylase really doing its job? | + | |
| + | I next went on the compare the sequence to [http://edwards.sdsu.edu/halophiles/#RastAnnotation halophile genomes that have already been annotated] in order to determine if the function of similar sequences was the same. I started with Haloferax volcanii using the GeneBank annotation data and found 1 histone deacetylase gene and 3 histone acetylases. I think it is important to note that while searching the list of functional genes for our species I found no acetyltransferase genes, which asks the question. . . What is placing the acetyl groups on the histone that the deacetylase is removing OR is the deacetylase really doing its job? | ||
Below is the data from the blast2 results comparing the histone deacetylase sequences from our species and Haloferax volcanii. | Below is the data from the blast2 results comparing the histone deacetylase sequences from our species and Haloferax volcanii. | ||
Revision as of 00:03, 8 September 2009
Contents
Histone Deacetylase (644029844)
What is this gene?
The Adopt a Genome Project claims that this gene's functionality is as a [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644029844 deacetylase, histone deacetylase/acetoin utilization protein.
These two proteins facilitate the removal of acetyl groups from histones in eukarya and are share 9 motifs with similar genes/proteins in archaea and eubacteria [Leipe and Landsman]. This is where our species comes into play: as an archaea we should ask ourselves where this gene comes from and whether or not the normal functioning of the gene in eukaraya is also seen in our species. If so this means that our archaea has the ability to epigenetically alter transcription of specific genes. This would be an interesting study to show evolutionary patterns, as bacteria do not normally posses histone deacetylases.
What is a Histone Deacetylase?
Histone deacetylase (HDAC) and histone acetyltransferase (HAT) are enzymes that influence transcription by removing or adding acetyl groups to lysine located near the amino termini of histone proteins. When HAT adds an acetyl group to a histone transcriptional activity changes, whereas deactylation leads to gene silencing. "HDACs are also involved in the reversible acetylation of non-histone proteins" [Vinci-Biochem].
Histone Acetylation in eukarya is a form of epigenetic regulation, where the density of chromatin is affected leading to changes in transcriptional rates.
What I found in Exploring this Gene
In completing a blastn search for this gene sequence I found many different hits from other halophiles but none of the hits described any sort of function. The results only showed that this sequence is often found in other halophiles, such as Haloarcula marismortui.
I next went on the compare the sequence to halophile genomes that have already been annotated in order to determine if the function of similar sequences was the same. I started with Haloferax volcanii using the GeneBank annotation data and found 1 histone deacetylase gene and 3 histone acetylases. I think it is important to note that while searching the list of functional genes for our species I found no acetyltransferase genes, which asks the question. . . What is placing the acetyl groups on the histone that the deacetylase is removing OR is the deacetylase really doing its job?
Below is the data from the blast2 results comparing the histone deacetylase sequences from our species and Haloferax volcanii.
