Difference between revisions of "Methytransferases and RNAi Pathways"

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== DNA methyltransferase ==
 
== DNA methyltransferase ==
 
<ul>
 
<ul>
−
<li>MET1 DNA methyltransferase</li>
+
I am interested in examining the conservation of these enzymes and short interfering RNA across plant genomes. I will examine paralogs and orthologs of these genes and compare and contrast the elements of both <i>de novo</i> and maintenance methylation pathways. I would also love to isolate possible methylation sites across the <i>Vaccinium corymbosum</i> genome. I hope to find differences in methylation pathways between plant species at both the protein and epigenetic levels. A phylogenetic analysis from the methylation pathway standpoint will follow.
 +
<br>
 +
<br>
 +
<li>METHYLTRANSFERASE1 [http://www.ncbi.nlm.nih.gov/protein/NP_199727.1 (MET1)]</li>
 
MET1 is responsible for maintaining CG methylation.  
 
MET1 is responsible for maintaining CG methylation.  
−
<li>DRM1 and DRM2 DNA methyltransferase</li>
+
<li>CHROMOMETHYLASE3 [http://www.ncbi.nlm.nih.gov/protein/NP_177135.1 (CMT3)] </li>
−
DRM2 is the primary enzyme implicated in the RNAi mediated methylation pathway. Other  The enzyme constantly targets CHH sites [http://www.ncbi.nlm.nih.gov/pubmed/19384058 (Widman <i>et. al</i>, 2009)]. DRM2 is expressed at higher levels than DRM1 and is the main enzyme involved in <i>de novo</i> methylation [http://books.google.com/books?id=aBlXT_Y7JCwC&pg=PA3&lpg=PA3&dq=drm1+methylation&source=bl&ots=Cy4nSsNyPE&sig=ei_5_6t6j9cLBObpxE7coRyO1OI&hl=en&ei=5vlHTcagB4XVgQet56WfBg&sa=X&oi=book_result&ct=result&resnum=6&sqi=2&ved=0CDkQ6AEwBQ#v=onepage&q=drm1%20methylation&f=false (Meyer, 2005)].
+
Chromomethylase3 maintains methylation in non-Cg sequences redundantly with DRM1/2 [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001182;jsessionid=35538162FE4C85BD00D0578063186ED0.ambra01 (Henderson <i>et. al</i>, 2006)].
 +
<li>DOMAINS REARRANGED METHYLTRANSFERASE1 [http://www.ncbi.nlm.nih.gov/protein/NP_197042.2 (DRM1)] and [http://www.ncbi.nlm.nih.gov/protein/NP_196966.2 (DRM2)]</li>
 +
DRM2 is the primary enzyme implicated in the RNAi mediated methylation pathway. The enzyme constantly targets CHH sites [http://www.ncbi.nlm.nih.gov/pubmed/19384058 (Widman <i>et. al</i>, 2009)]. DRM2 is expressed at higher levels than DRM1 and is the main enzyme involved in <i>de novo</i> methylation [http://books.google.com/books?id=aBlXT_Y7JCwC&pg=PA3&lpg=PA3&dq=drm1+methylation&source=bl&ots=Cy4nSsNyPE&sig=ei_5_6t6j9cLBObpxE7coRyO1OI&hl=en&ei=5vlHTcagB4XVgQet56WfBg&sa=X&oi=book_result&ct=result&resnum=6&sqi=2&ved=0CDkQ6AEwBQ#v=onepage&q=drm1%20methylation&f=false (Meyer, 2005)].
  
−
<li>DRM3 DNA methytransferase</li>
+
<li>DOMAINS REARRANGED METHYLTRANSFERASE3 (DRM3)</li>
 
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001182;jsessionid=35538162FE4C85BD00D0578063186ED0.ambra01 Henderson <i>et. al</i> (2006)] discovered that DRM3 is required for non-CG DNA methylation. DRM3 is a catalytically mutated paralog of DRM2. The activity of DRM2 is dependent on DRM3 and a UBA binding domain [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965745/ (Henderson <i>et. al</i>, 2010)]. Henderson <i>et. al</i> (2006) tested two T-DNA insertion strains (drm3-1 and drm3-2), finding a reduction of methylation of MEA-ISR. After performing a southern blot on the Msp1 (methyl-sensitive restriction enzyme) digested MEA-ISR repeat and sequencing samples of this DNA using the bisulfite method, the researchers concluded that DRM3 is necessary for proper DRM2 functioning.
 
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001182;jsessionid=35538162FE4C85BD00D0578063186ED0.ambra01 Henderson <i>et. al</i> (2006)] discovered that DRM3 is required for non-CG DNA methylation. DRM3 is a catalytically mutated paralog of DRM2. The activity of DRM2 is dependent on DRM3 and a UBA binding domain [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965745/ (Henderson <i>et. al</i>, 2010)]. Henderson <i>et. al</i> (2006) tested two T-DNA insertion strains (drm3-1 and drm3-2), finding a reduction of methylation of MEA-ISR. After performing a southern blot on the Msp1 (methyl-sensitive restriction enzyme) digested MEA-ISR repeat and sequencing samples of this DNA using the bisulfite method, the researchers concluded that DRM3 is necessary for proper DRM2 functioning.
 
<br>
 
<br>
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----
 
----
  
−
== Other proteins involved in RNAi and chromatin   ==
+
== Other proteins/RNA involved in RNAi and chromatin processing  ==
 
<ul>
 
<ul>
−
<li>NUCLEAR RNA POLYMERASE D1 (NRPD1)</li>  
+
<li>NUCLEAR RNA POLYMERASE D1 [http://www.ncbi.nlm.nih.gov/protein/NP_176490.2 (NRPD1)]</li>  
−
<li>NUCLEAR RNA POLYMERASE E1 (NRPE1)</li>  
+
<li>NUCLEAR RNA POLYMERASE E1 [http://www.ncbi.nlm.nih.gov/protein/79571777 (NRPE1)]</li>  
−
<li>RNA DEPENDENT RNA POLYMERASE2 (RDR2) </li>
+
<li>RNA DEPENDENT RNA POLYMERASE2 [http://www.ncbi.nlm.nih.gov/protein/NP_192851.1 (RDR2)]</li>
−
<li>DICER-LIKE3 (DCL3)</li>
+
<li>DICER-LIKE3 [http://www.ncbi.nlm.nih.gov/protein/YP_002497289.1 (DCL3)]</li>
−
<li>ARGONAUTE4 (AGO4)</li>
+
<li>ARGONAUTE4 [http://www.ncbi.nlm.nih.gov/protein/NP_565633.1 (AGO4)]</li>
−
<li>DEFECTIVE IN RNA DIRECTED DNA METHYLATION 1 (DRD1)</li>
+
<li>DEFECTIVE IN RNA DIRECTED DNA METHYLATION 1 [http://www.ncbi.nlm.nih.gov/protein/NP_179232.1 (DRD1)]</li>
 
<li>DEFECTIVE IN MERISTEM SILENCING1 (DMS1)</li>
 
<li>DEFECTIVE IN MERISTEM SILENCING1 (DMS1)</li>
 
<li>INVOLVED IN DE NOVO 2 (IND2)</li>
 
<li>INVOLVED IN DE NOVO 2 (IND2)</li>
−
<li>SUPPRESSOR OF VARIEGATION 3-9 HOMOLOGUE 2 (SUVH2)</li>
+
<li>SUPPRESSOR OF VARIEGATION 3-9 HOMOLOGUE 2 [http://www.ncbi.nlm.nih.gov/protein/AAK28967.1 (SUVH2)] [http://www.ncbi.nlm.nih.gov/protein/AAK28967.1 (SUVH2 homolog)]</li>
−
<li>SUPPRESSOR OF VARIEGATION 3-9 HOMOLOGUE 9 (SUVH9)</li>
+
<li>SUPPRESSOR OF VARIEGATION 3-9 HOMOLOGUE 9 [http://www.ncbi.nlm.nih.gov/protein/NP_001031625.1 (SUVH9)]</li>
 
</ul>
 
</ul>
−
<br>
 
 
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001182;jsessionid=35538162FE4C85BD00D0578063186ED0.ambra01 (Henderson <i>et. al</i>, 2006)]
 
[http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001182;jsessionid=35538162FE4C85BD00D0578063186ED0.ambra01 (Henderson <i>et. al</i>, 2006)]
 +
 +
== Other Links and Resources ==
 +
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC197300/
 +
<br><br>
 +
http://www.mcdb.ucla.edu/Research/Jacobsen/Labwebsite/PDFPublication/DRMgenePNAS.pdf<br><br>
 +
http://www.ncbi.nlm.nih.gov/pubmed/19384058<br><br>
 +
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001182;jsessionid=35538162FE4C85BD00D0578063186ED0.ambra01<br><br>
 +
http://books.google.com/books?id=aBlXT_Y7JCwC&pg=PA3&lpg=PA3&dq=drm1+methylation&source=bl&ots=Cy4nSsNyPE&sig=ei_5_6t6j9cLBObpxE7coRyO1OI&hl=en&ei=5vlHTcagB4XVgQet56WfBg&sa=X&oi=book_result&ct=result&resnum=6&sqi=2&ved=0CDkQ6AEwBQ#v=onepage&q=drm1%20methylation&f=false<br><br>
 +
http://www.pnas.org/content/107/19/8689.full.pdf<br><br>
 +
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0000067<br><br>
 +
http://www.mcdb.ucla.edu/research/jacobsen/labwebsite/PDFPublication/MethylationConservation.pdf

Latest revision as of 13:39, 1 February 2011

PlantGDB Comparison Tools

DNA methyltransferase

    I am interested in examining the conservation of these enzymes and short interfering RNA across plant genomes. I will examine paralogs and orthologs of these genes and compare and contrast the elements of both de novo and maintenance methylation pathways. I would also love to isolate possible methylation sites across the Vaccinium corymbosum genome. I hope to find differences in methylation pathways between plant species at both the protein and epigenetic levels. A phylogenetic analysis from the methylation pathway standpoint will follow.

  • METHYLTRANSFERASE1 (MET1)

    • MET1 is responsible for maintaining CG methylation.

  • CHROMOMETHYLASE3 (CMT3)

    • Chromomethylase3 maintains methylation in non-Cg sequences redundantly with DRM1/2 (Henderson et. al, 2006).

  • DOMAINS REARRANGED METHYLTRANSFERASE1 (DRM1) and (DRM2)

    • DRM2 is the primary enzyme implicated in the RNAi mediated methylation pathway. The enzyme constantly targets CHH sites (Widman et. al, 2009). DRM2 is expressed at higher levels than DRM1 and is the main enzyme involved in de novo methylation (Meyer, 2005).

  • DOMAINS REARRANGED METHYLTRANSFERASE3 (DRM3)

    • Henderson et. al (2006) discovered that DRM3 is required for non-CG DNA methylation. DRM3 is a catalytically mutated paralog of DRM2. The activity of DRM2 is dependent on DRM3 and a UBA binding domain (Henderson et. al, 2010). Henderson et. al (2006) tested two T-DNA insertion strains (drm3-1 and drm3-2), finding a reduction of methylation of MEA-ISR. After performing a southern blot on the Msp1 (methyl-sensitive restriction enzyme) digested MEA-ISR repeat and sequencing samples of this DNA using the bisulfite method, the researchers concluded that DRM3 is necessary for proper DRM2 functioning.
    DRM3figure.png
    (A) Southern blots hybridized for the MEA-ISR repeat using DNA digested with the methyl-sensitive restriction enzyme MspI. The 4.3 kb band and 2 kb bands represent digested and undigested DNA respectively. (B) Graphical representation of bisulfite sequencing at MEA-ISR with % cytosine methylation shown for each genotype. CG sequence contexts are shaded black, CHG are shaded grey and white represents CHH. The 95% confidence limits shown are given by the Wilson score interval. (C) Graphical representation of bisulfite sequencing at the methylated promoter repeats of the FWA endogene with % cytosine methylation shown for each genotype and shaded according to sequence context as in (B). (D) Quantitative PCR measurement of AtSN1 genomic DNA following restriction endonuclease digestion with DNA methylation sensitive enzyme HaeIII. The value on the y-axis represents the ratio of DNA measured by quantitative PCR with and without HaeIII digestion. The data represents three biological replicates and the error bars represent standard error.

Other proteins/RNA involved in RNAi and chromatin processing

  • NUCLEAR RNA POLYMERASE D1 (NRPD1)
  • NUCLEAR RNA POLYMERASE E1 (NRPE1)
  • RNA DEPENDENT RNA POLYMERASE2 (RDR2)
  • DICER-LIKE3 (DCL3)
  • ARGONAUTE4 (AGO4)
  • DEFECTIVE IN RNA DIRECTED DNA METHYLATION 1 (DRD1)
  • DEFECTIVE IN MERISTEM SILENCING1 (DMS1)
  • INVOLVED IN DE NOVO 2 (IND2)
  • SUPPRESSOR OF VARIEGATION 3-9 HOMOLOGUE 2 (SUVH2) (SUVH2 homolog)
  • SUPPRESSOR OF VARIEGATION 3-9 HOMOLOGUE 9 (SUVH9)

(Henderson et. al, 2006)

Other Links and Resources

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC197300/

http://www.mcdb.ucla.edu/Research/Jacobsen/Labwebsite/PDFPublication/DRMgenePNAS.pdf

http://www.ncbi.nlm.nih.gov/pubmed/19384058

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001182;jsessionid=35538162FE4C85BD00D0578063186ED0.ambra01

http://books.google.com/books?id=aBlXT_Y7JCwC&pg=PA3&lpg=PA3&dq=drm1+methylation&source=bl&ots=Cy4nSsNyPE&sig=ei_5_6t6j9cLBObpxE7coRyO1OI&hl=en&ei=5vlHTcagB4XVgQet56WfBg&sa=X&oi=book_result&ct=result&resnum=6&sqi=2&ved=0CDkQ6AEwBQ#v=onepage&q=drm1%20methylation&f=false

http://www.pnas.org/content/107/19/8689.full.pdf

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0000067

http://www.mcdb.ucla.edu/research/jacobsen/labwebsite/PDFPublication/MethylationConservation.pdf

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