ࡱ > ~ #` bjbj\.\. >D >D 4
4
4
4
$ X
? x
L
$ 5 h 4
^
4 4
| | | 4
| 4 | | |
l
WD0 4
. . | 0 ? | { \ { | { | x
0 " | 7 S
r
? 4 4 4 4 d Fig S2 Sequence properties of methylated CGIs. Bock and colleagues determined a number of DNA sequence features which are correlated with DNA methylation at CGIs ADDIN EN.CITE Bock200611311317Bock, C.Paulsen, M.Tierling, S.Mikeska, T.Lengauer, T.Walter, J.Max-Planck-Institut fur Informatik, Saarbrucken, Germany. cbock@mpi-inf.mpg.deCpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structurePLoS GenetPLoS Genete2623*CpG IslandsDNA/chemistry*DNA MethylationGenome, HumanHumansLymphocytes/*cytologyModels, GeneticModels, Statistical*Nucleic Acid Conformation*Repetitive Sequences, Nucleic AcidResearch Support, Non-U.S. Gov'tSulfites2006Mar16520826http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16520826 Using methylation data based on Yamada 2004 (#122). Identify computational predicted features that can potentially id methylateable CpG Islands - reasonable correlations but not particularily great? [1]. Here we compare the sequence attributes of the methylated and total CpG Island sets with respect to DNA structure (stacking energy and base twist) and specific repeats (TGTG/CACA). Methylated CpG islands show small but significant increase in stacking energy relative to all CGIs (p-value < 0.001). In contrast we found no significant difference in the base twist of methylated CGIs.
TGTG/CACA specific repeats were found to be significantly enriched in methylated CGIs (p-value < 0.001; see text for discussion). In contrast, all repetitive elements (as outlined in Repbase ADDIN EN.CITE Jurka200518718717Jurka, J.Kapitonov, V. V.Pavlicek, A.Klonowski, P.Kohany, O.Walichiewicz, J.Genetic Information Research Institute, Mountain View, CA 94043, USA. jurka@girinst.orgRepbase Update, a database of eukaryotic repetitive elementsCytogenet Genome ResCytogenet Genome Res462-71101-4AnimalsDNA/geneticsDNA Transposable Elements*Databases, Nucleic AcidEvolution, MolecularHumansRepetitive Sequences, Nucleic Acid/*genetics200516093699http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16093699 [2]) were found to be marginally depleted in methylated CGIs (p-value < 0.01, Wilcoxon rank sum test (n=4082 and 10236)
Stacking energy and base twist were calculated using the EMBOSS btwisted program with default settings ADDIN EN.CITE Rice200018518517Rice, P.Longden, I.Bleasby, A.The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK CB10 1SA.EMBOSS: the European Molecular Biology Open Software SuiteTrends GenetTrends Genet276-7166*Internet*Molecular BiologySequence Alignment/methods*SoftwareUser-Computer Interface2000Jun10827456http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10827456 [3]. All distributions were tested for parametric distribution by the the Shapiro-Wilk test of normality. Non parametric significance values were determined using the Wilcoxon rank sum test (n=4082 and 10236).
ADDIN EN.REFLIST 1. Bock C, Paulsen M, Tierling S, Mikeska T, Lengauer T, et al. (2006) CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet 2: e26.
2. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
3. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
/ 1 x { | ʿuggYKY h` CJ OJ QJ ^J aJ hl` CJ OJ QJ ^J aJ h/<