Comparative (Computational) Analysis of the DNA Methylation Status of Trinucleotide Repeat Expansion Diseases

Table 3

Comparison of MEME results with patterns found in this study.

(a) 10 best 5 bp motifs in variably methylated regions

Pattern	MEME detail positive or negative strand	Our software variably methylated
TGTTT	FXN+, FMR1+	FMR1+, FXN+
AAACT	FXN++−	FXN++−
TATTT	FXN++	FXN++
TCCAA	FXN+DMPK−	FXN+DMPK+
TCGAA	DMPK+DMPK−	DMPK+DMPK−
CTGAG	FMR1 − −	DMPK+FMR1+FMR1− −
CTGAA	FMR1−DMPK+	DMPK+FMR1−
GAGAG	FXN−FMR1+	FMR1++FXN −−
TA[CG]AA	DMPK−DMPK+	DMPK−DMPK+FXN−
ACCCA	DMPK− −	DMPK − −

(b) 10 best 5 bp motifs in always methylated regions

Pattern	MEME detail positive or negative strand	Our software always methylated
AGGGG	FXN_AM_1++FMR1+−−	FMR1+−−FXN_AM_1++
CCAGC	FXN_AM_1−FMR1−	FMR1 +−− FXN_AM_1−
CTGGC	FXN_AM_2+FMR1+	FMR1 +++ FXN+
CCACC	FXN_AM_2−FMR1+	FMR1 ++ FXN_AM_2−
CCTCA	FMR1 −−	FMR1+ −−−
CCGCC	FXN_AM_1−FMR1+	FXN_AM_1−FMR1+
AGCAC	FXN_AM_2−FMR1−	FXN_AM_2−FMR1+++−
AGTTG	FMR1++	FMR1+++FMR1 −−
TAGCA	FMR1−FMR+	FMR1 ++−−
AGAAA	FXN_AM_2+FMR1++−−−−	FXN_AM_2+FMR1++−−−−

(c) 10 best 5 bp motifs in never methylated region

Pattern	MEME detail positive or negative strand	Our software never methylated
TTTGC	DMPK++−	DMPK ++−−−
TTCTT	DMPK++	DMPK+++
AGGCA	DMPK−+	DMPK+−
TT[AT]CT	DMPK ++	DMPK++++
CCATC	DMPK+−	DMPK+−
CAGGC	DMPK++	DMPK ++−−
CAGAC	DMPK−+	DMPK+−
TGACG	DMPK++	DMPK++
ACC[AT]A	DMPK−+	DMPK+−
CTGGG	DMPK++	DMPK++

Key:
+ Positive strand.
− Negative strand.
FXN_AM_1 and FXN_AM_2 are two separated regions with always methylated CpG sites.
Bold: Motif that MEME does not report all occurrences.