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In most tissues, close to 100% of DNA methylation occurs at CpG sites. This provides a straightforward mechanism for epigenetic inheritance. Since C and G are complementary, both strands have the CpG site at the same locus and methylation is either present on both strands or on neither. During replication, each daughter DNA molecule inherits a parent strand ...


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Spermatogenesis (Beginning to end): 64 +- 8 days (range 42 to 76) There is considerable individual variation. This includes time in epididymis. Amann 2008 argue for 74 days based on early study by Clermont 1972. Also argue that biopsies are still needed on top of radiolabelling. Substages: Calculated from Amann 2008, Figure 1 using percent time in 16 ...


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CG methylation has long been associated with gene silencing due to the generally negative correlation between gene promoter methylation and transcription levels. When CG methylation occurs in the promoter or enhancer region of animals (where these 'CpG islands' tend to be), methylation seems to impede (to some extent) transcription factor (TF) binding. ...


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The problem is that for most sequencing operations you nowadays still need more than one cell - even though this will change soon. Accordingly, you have to sample cells from a tissue which often, if not usually, contains more than one cell type, see e.g. this picture from a lung tissue from the Wikipedia article on tissues linked above: It is not always ...


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I looked into this and if the effect is real, which it sounds like it is, it may be 5-formylcytosine. Methylcytosine oxidizes into hydroxymethylcytosine, which reacts with bisulphite exactly like you expect (identically). Hydroxymethylcytosine further oxidizes to 5-formylcytosine, which behaves like unmodified cytosine (i,e. deaminates to form U). TET ...


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21joanna12, look into snRNPs. These are parts of the splicosomal apparatus and some of them (the U1 and U2, U11 and U12 snRNPs) are also the guideposts that bind near the splice junctions at the end of introns. These help guide the splicing apparatus to the splice sites. There are also proteins that bind RNA and interact with the splicing apparatus to ...


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According to this instruction it can be done for 1 hour but this is for large plasmids. I agree with Chris that it should not be of a problem. Alternatively you can setup your 37°C DpnI incubation step in a PCR machine and after however long that is recommended, you can set the PCR machine to cool to 4°C automatically, that way you can leave it there for as ...


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I've got to dash off so I won't be able to give a fully in-depth answer today, but this basically boils down to the concept of CpG islands. Something like 70-80% of CpGs are methylated in humans, so if they were randomly scattered around the genome there is already a pretty high chance nearby CpGs are in the same state. However, because of CpG islands, ...


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Okay I'll try to put together a quick answer. First: 'How do you analyze DNA methylation data generated from the EPIC array from Illumina' The most common method to analyse DNA methylation is based on bisulfite conversion of DNA. This chemical converts the base cytosine (C) to uracil (U), which 'reads' the same as thymine (T), but it only works on non-...


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The "histone code" is not like the genetic code where one codon in an ORF always is translated to a single amino acid. It's closer to something like GC content or CpG islands: a single instance doesn't tell you anything, but enrichment over some finite window may be biologically significant. You may want to review the basics, starting with the Wikipedia ...


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For histone methylation , whether the marks are activating or repressive is determined predominately by which histone tail is modified at which position. DNA methylation by itself however is position dependent; in regulatory regions such as enhancers and promoters methylation tends to be repressive (at enhancers this is mostly mediated by being ...


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The use of RRBS instead of WGBS is mostly about coverage vs. cost. To confidently call methylation status at a cytosine residue, you need to have at least 10x sequencing coverage at that particular residue (ENCODE standards require at least 10x coverage for RRBS and 30x coverage for WGBS). To perform whole-genome bisulfite sequencing (WGBS) on large genomes ...


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The answer is relatively simple: Mature erythrocytes do not have a nucleus and thus you cannot study methylation patterns there. You can do this in young, developing erythrocytes which still have their nucleus.


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Generally, robust silencing by DNA methylation requires that all or most CG sites be methylated and that there are a good number of CG sites to methylate. (A 'good number' is relative to each species depending on CG content of the respective genome.) A promoter with ~10% of its CG sites methylated would not likely be silenced. However, the caveat with ...


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There is also a phenomena called hemimethylation where one of strand is methylated while the other one is unmethylated or vice versa. There have been various research questions associated with hemimethylation, you can find more about it in here: http://nathansheffield.com/wordpress/what-is-hemimethylated-dna/


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