Our Dirty Genuine Truth On The Ivacaftor

, 2012). The average read number of the CH group (10.0) is significantly smaller than that of the CG group (12.4, p value?Ipatasertib chromosome 11 (Figure?2B). Sex chromosomes are depleted in 5hmC, with little 5hmCs in the Y chromosome (Figure?2B). Depletion of 5mC and 5hmC (Szulwach et?al., 2011) in X chromosomes has been observed in neuronal tissues and stem cells. Together these results suggest a different epigenetic regulation mechanism between the autosomes and sex chromosomes. Tubulin In addition, we observed the highest 5hmC site density in the mitochondria genome in both CG and CH contexts (Figure?2B). Considering that mitochondria genomes are present in multiple copies in the cell, it remains inconclusive whether they are enriched in 5hmC. Nevertheless, inside mitochondria DNA, normalized CH 5hmC site density is nearly as high as the normalized CG 5hmC site density, whereas it is less than 1% of the latter for all other chromosomes (Figure?2B). A set of key DNA epigenetic components, including DNMT1, TET enzymes, and their products 5mC and 5hmC, were reported in mitochondria (Shock et?al., 2011). Our results further suggest that the prevalent pattern of hydroxymethylation, possibly methylation, in mitochondria Ivacaftor in vitro genome might exist in an unbiased manner toward CG or CH. Overall, our results suggest a different epigenome in the mitochondria than that in the nucleus. Most of the identified 5hmC sites reside in intergenic regions, followed by introns (Figure?2C). Compared with a base-resolution methylome map in the mouse ESCs (Stadler et?al., 2011) (Figure?S2B), 5hmCGs are slightly enriched in the intragenic regions and depleted in the intergenic regions. This is consistent with the previous findings using hMeDIP approaches (Ficz et?al., 2011). A gene-centric view of 5hmC as well as 5mC distribution in both DNA strands is shown in Figure?2D. There is no noticeable difference for the 5hmCG distribution between the sense and the antisense strands (Figure?2D). We normalized the 5hmCG site density by the 5mCG density, which accounts for the local substrate concentration effect presented to the TET enzymes. The normalized 5hmCG site density is reduced at the transcription start sites (TSSs) and 5�� UTR regions (Figure?2D), and a similar trend is observed for the 5hmCH site (data not shown).