Histone Deacetylase (Katie Richeson) - Revision history

MaCampbell: /* What is a Histone Deacetylase? */

2009-09-08T16:07:37Z

‎What is a Histone Deacetylase?

MaCampbell: /* What is a Histone Deacetylase? */

2009-09-08T16:07:18Z

‎What is a Histone Deacetylase?

Karicheson at 00:36, 8 September 2009

2009-09-08T00:36:16Z

Karicheson at 00:34, 8 September 2009

2009-09-08T00:34:06Z

Karicheson at 00:23, 8 September 2009

2009-09-08T00:23:25Z

Karicheson at 00:21, 8 September 2009

2009-09-08T00:21:41Z

Karicheson at 00:19, 8 September 2009

2009-09-08T00:19:41Z

Karicheson at 00:17, 8 September 2009

2009-09-08T00:17:43Z

Karicheson at 00:16, 8 September 2009

2009-09-08T00:16:15Z

Karicheson at 00:14, 8 September 2009

2009-09-08T00:14:13Z

← Older revision		Revision as of 16:07, 8 September 2009
Line 13:		Line 13:


−	Histone Acetylation in eukarya is a form of epigenetic regulation, where the density of chromatin is affected leading to changes in transcriptional rates.	+	Histone Acetylation in eukarya is a form of epigenetic regulation, where the density of chromatin is affected leading to changes in transcriptional rates.<br>
	[http://www.nature.com/nrd/journal/v1/n4/images/nrd772-f1.jpg[[Image:histonepicture.jpg]]]		[http://www.nature.com/nrd/journal/v1/n4/images/nrd772-f1.jpg[[Image:histonepicture.jpg]]]

← Older revision		Revision as of 16:07, 8 September 2009
Line 10:		Line 10:
	[http://www.rcsb.org/pdb/explore.do?structureId=3HGQ[[Image:deacetylase.jpg]]]		[http://www.rcsb.org/pdb/explore.do?structureId=3HGQ[[Image:deacetylase.jpg]]]

−	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" [[http://www.vincibiochem.it/HistoneDeacetylase.htm Vinci-Biochem]].	+	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" [[http://www.vincibiochem.it/HistoneDeacetylase.htm Vinci-Biochem]].<br>

@@ Line 16: / Line 16: @@
 [http://www.nature.com/nrd/journal/v1/n4/images/nrd772-f1.jpg[[Image:histonepicture.jpg]]]
-== What I found in Exploring this Gene ==
+== Blastn Search ==
 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].
 When I did a blastx search using the sequence of our specie's histone deacetylase multiple histone deacetylase protein super family alignments appeared (this is also where I got the amino acid sequence from the nucleotide sequence for this gene in our species).  Below is a picture of the matches from the blastx results:
@@ Line 24: / Line 25: @@
 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 [http://edwards.sdsu.edu/halophiles/Haloferax_volcanii_ATCC_29605/RAST_Annotation/309800.12.gbk  Haloferax volcanii using the GenBank annotation data] and found 1 histone deacetylase gene and 3 histone acetylases.  I think it is important to note that while searching the [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=TaxonDetail&page=proteinCodingGenes&taxon_oid=643886133 list of functional protein genes for our species] I found no histone 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?
@@ Line 35: / Line 37: @@
 [[Image:blastpHM.jpg]]
+==Blastp Alignment with Human Histone Deacetylase Gene==
 I also searched the human genome to determine how many histone deacetylase genes existed and did a blastp alignment search between these two genes. I used Ensembl to look up [http://www.ncbi.nlm.nih.gov:80/nuccore/AJ011972?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum  amino acid sequences for histone deacetylases] in the human genome and found a few [http://www.ensembl.org/Homo_sapiens/Search/Summary?species=Homo_sapiens;idx=;q=histone%20deacetylase results]. The blastp results between one human histone deacetylase gene and the histone deacetylase gene in out species are as follows:
 [[Image:human.jpg]]

← Older revision		Revision as of 00:34, 8 September 2009
Line 36:		Line 36:


−	Finally I explored the GC content of this gene to determine if it originates from another genome. The GC content of our species' genome is around	+	Finally I explored the GC content of this gene to determine if it originates from another genome. The GC content of our species' genome is around [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2500395343 65%]. The GC content for this gene is [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644029844 68%]. The similarity between these two GC content percentages seems to indicate that this gene is not an alien gene resulting from some sort of lateral transfer, but it does not rule out that this gene may be an ortholog.
		+
		+	I also searched the human genome to determine how many histone deacetylase genes existed and did a blastp alignment search between these two genes. I used Ensembl to look up [http://www.ncbi.nlm.nih.gov:80/nuccore/AJ011972?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum amino acid sequences for histone deacetylases] in the human genome and found a few [http://www.ensembl.org/Homo_sapiens/Search/Summary?species=Homo_sapiens;idx=;q=histone%20deacetylase results]. The blastp results between one human histone deacetylase gene and the histone deacetylase gene in out species are as follows:
		+
		+	[[Image:human.jpg]]

@@ Line 30: / Line 30: @@
 [[Image:blastpHV.jpg]]
-I did the same paralog search in the halophile Haloferax mediteranei from Spain using [http://edwards.sdsu.edu/halophiles/Haloferax_mediteranei_ATCC_33500/RAST_Annotation/523841.3.gbk GenBank annotation results]. This genome included one histone deacetylase and 2 histone acetyltransferases. The blastp alignment results are seen below:
 [[Image:blastpHM.jpg]]

← Older revision		Revision as of 00:21, 8 September 2009
Line 30:		Line 30:
	[[Image:blastpHV.jpg]]		[[Image:blastpHV.jpg]]

−	I did the same paralog search in the halophile Haloferax mediteranei from Spain using [http://edwards.sdsu.edu/halophiles/Haloferax_mediteranei_ATCC_33500/RAST_Annotation/523841.3.gbk GenBank annotation results]. The blastp alignment results are seen below.	+	I did the same paralog search in the halophile Haloferax mediteranei from Spain using [http://edwards.sdsu.edu/halophiles/Haloferax_mediteranei_ATCC_33500/RAST_Annotation/523841.3.gbk GenBank annotation results]. This genome included one histone deacetylase and 2 histone acetyltransferases. The blastp alignment results are seen below:
		+
		+	[[Image:blastpHM.jpg]]

← Older revision		Revision as of 00:19, 8 September 2009
Line 30:		Line 30:
	[[Image:blastpHV.jpg]]		[[Image:blastpHV.jpg]]

−	I did the same paralog search in the halophile	+	I did the same paralog search in the halophile Haloferax mediteranei from Spain using [http://edwards.sdsu.edu/halophiles/Haloferax_mediteranei_ATCC_33500/RAST_Annotation/523841.3.gbk GenBank annotation results]. The blastp alignment results are seen below.

← Older revision		Revision as of 00:17, 8 September 2009
Line 29:		Line 29:

	[[Image:blastpHV.jpg]]		[[Image:blastpHV.jpg]]
		+
		+	I did the same paralog search in the halophile

← Older revision		Revision as of 00:16, 8 September 2009
Line 26:		Line 26:
	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 [http://edwards.sdsu.edu/halophiles/Haloferax_volcanii_ATCC_29605/RAST_Annotation/309800.12.gbk Haloferax volcanii using the GenBank annotation data] and found 1 histone deacetylase gene and 3 histone acetylases. I think it is important to note that while searching the [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=TaxonDetail&page=proteinCodingGenes&taxon_oid=643886133 list of functional protein genes for our species] I found no histone 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 [http://edwards.sdsu.edu/halophiles/Haloferax_volcanii_ATCC_29605/RAST_Annotation/309800.12.gbk Haloferax volcanii using the GenBank annotation data] and found 1 histone deacetylase gene and 3 histone acetylases. I think it is important to note that while searching the [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=TaxonDetail&page=proteinCodingGenes&taxon_oid=643886133 list of functional protein genes for our species] I found no histone 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 protein sequences from our species and Haloferax volcanii.	+	Below is the data from the blast2 results comparing the histone deacetylase protein sequences from our species and Haloferax volcanii. They are 78% the same when positives are taken into account. I would say that they are certainly similar but not extremely similar.
		+
		+	[[Image:blastpHV.jpg]]

← Older revision		Revision as of 00:14, 8 September 2009
Line 20:		Line 20:

	When I did a blastx search using the sequence of our specie's histone deacetylase multiple histone deacetylase protein super family alignments appeared (this is also where I got the amino acid sequence from the nucleotide sequence for this gene in our species). Below is a picture of the matches from the blastx results:		When I did a blastx search using the sequence of our specie's histone deacetylase multiple histone deacetylase protein super family alignments appeared (this is also where I got the amino acid sequence from the nucleotide sequence for this gene in our species). Below is a picture of the matches from the blastx results:
		+
	[[Image:blastx.jpg]]		[[Image:blastx.jpg]]