DNA甲基化功能全解.pptVIP

RRBS (procedure) : RRBS (assessment) : Advantages Enrichment of CpGs Low sample input Disadvantages Restriction enzyme limitation BS-seq flaws BS-seq, TAB-seq and oxBS-seq--TET oxygenases BS-seq, TAB-seq and oxBS-seq--scheme BS-seq, TAB-seq and oxBS-seq--result Bisulfite Sequencingmapping schemes sequence changes: Problems: Searching space is significantly increased (Waston Crick) vs (BSW, BSWR, BSC, BSCR) Sequence complexity is reduced C to T mapping is asymmetric (complicates the matching process) Problems: Bismark scheme: BSMAP scheme: BSMAP scheme: Thank you! For BSW and BSC, C-poor (C - T) For BSWR and BSCR, G-poor (G - A) CHG, CHH : H represents A, C, or T How to handle the four bisulfite strands? One read: four alignments (original - Watson, original - Crick, reverse - Watson, reverse - Crick). 1. Hash the genomes. Using the original seed and bisulfite variants as keys and corresponding coordinates in the reference genome as values 2. Mask the corresponding reference sequence. (C - 01, A/T/G - 11) 3. AND operation, consider the converted unmethylated C. 4. XOR operation, count mismatches. * DNA methylation DNA甲基化功能 A few data human genome :about 28 milion CpGs 60–80% are generally methylated. Less than 10% of CpGs occur in CG-dense regions that are termed CpG islands; Half of CGI occur at gene body. A few knowledge 1.Three conserved enzymes DNA methyltransferase 1 (DNMT1): DNA methylation maintenance DNMT3A and DNMT3B:de novo methylation DNMT3L:is a catalytically inactive homologue of DNMT3A and DNMT3B 2.Demethylation:thymidine DNA glycosylase (TDG) ten eleven translocation methylatosine dioxygenase(TET) activation-induced cytodine deaminase(AID) The many roles of DNA methylation DNMT1 DNMT3A/B Marking active regulatory elements TF Stadler et al, Nature, 2011 Imprinting ♀ ♂ Brandeis et al, EMBO J, 1993 Alternative promoter regulation Maunakea et al, Nature, 2010 Silencing of repeats Alu/LINE/SINE Walsh et al, Nat Genetics, 1998 Gene silen