Steven Roberts more dmr  almost 9 years ago

Commit id: 9be5bc6d152f7f4a1765df00c1dbbdddf77eb939

deletions | additions      

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```  scaffold481 576986 578532 -3  scaffold247 141885 142442 -3  scaffold247 144031 144583 -2  scaffold1518 212680 213736 -3  scaffold853 46186 46496 -2  scaffold406 419330 419384 -2  scaffold406 419005 419060 -2  scaffold406 418360 418767 -2  scaffold394 555813 556224 -2  scaffold247 144031 144583 -2  scaffold242 75918 76344 -2  scaffold142 656144 656735 -2  scaffold12 243960 244376 -2  scaffold257 1235165 1235481 +2 

Significant hypomethylation is also present within the intron of [Tenascin](http://www.uniprot.org/uniprot/K1PZ30), a glycoprotein expressed in the extracellular matrix during stress.  ![scaffold1518_212680](./figures/scaffold1518_212680.png) ---  We also found a DMR upstream of [_E3 ubiquitin-protein ligase UHRF1_](http://www.ncbi.nlm.nih.gov/protein?cmd=Retrieve&dopt=GenPept&list_uids=405967132). Interestingly this is a protein that **bridges DNA methylation and chromatin modification**.   "Specifically recognizes and binds hemimethylated DNA at replication forks via its YDG domain and recruits DNMT1 methyltransferase to ensure faithful propagation of the DNA methylation patterns through DNA replication. In addition to its role in maintenance of DNA methylation, also plays a key role in chromatin modification: through its tudor-like regions and PHD-type zinc fingers, specifically recognizes and binds histone H3 trimethylated at 'Lys-9' (H3K9me3) and unmethylated at 'Arg-2' (H3R2me0), respectively, and recruits chromatin proteins. Enriched in pericentric heterochromatin where it recruits different chromatin modifiers required for this chromatin replication. Also localizes to euchromatic regions where it negatively regulates transcription possibly by impacting DNA methylation and histone modifications. Has E3 ubiquitin-protein ligase activity by mediating the ubiquitination of target proteins such as histone H3 and PML. It is still unclear how E3 ubiquitin-protein ligase activity is related to its role in chromatin in vivo." ~http://www.uniprot.org/uniprot/Q96T88  While not classified as a differentially expressed gene, there does appear to be a trend towards increased expression upon heat stress. This occurrence would follow the traditional model where decreased methylation in the promoter region is associated with increased expression.  ![scaffoldscaffold853_46186](./figures/scaffold853_46186.png)   ---  There were three features identified that are in fact within an intron of [_Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial_](http://www.uniprot.org/uniprot/K1RSA6), and enzyme involved in leucine and isovaleric acid catabolism.  ![scaffold406](./figures/scaffold406.png)   ---  In an another example of a DMR associated with a differentially expressed gene, a DMR that span an intron and exon within [_Myosin heavy chain, striated muscle_](http://www.uniprot.org/uniprot/K1RSS3). In this case the gene is expressed at a lower level upon heat stress. It is also worth pointing out this gene has very limited methylation overall based on other studies we have done.   ![scaffold394_555813](./figures/scaffold394_555813.png)  ---  Another interesting DMR was found in [_Methylated-DNA--protein-cysteine methyltransferase_](http://www.uniprot.org/uniprot/K1RE67).   ![scaffold242_75918](./figures/scaffold242_75918.png)