How to interpret Methylation Sensitive Amplified Polymorphism (MSAP) profiles?

BMC Genomic Data

Table 1 Frequency, effect on cleavage and expected MSAP profile of ten different methylated forms of CCGG site

Site	C C G G	³C^mC G G	C^mC G G	C^mC G G	C^mC G G	^mC C G G	^mC C G G	^mC C G G	^mC^mC G G	^mC^mC G G
	G G C C	G G C C	G G^mC C	G G^mC^mC	G G C^mC	G G C C	G G C^mC	G G^mC^mC	G G C C	G G^mC^mC
¹Frequency	Low	Low	High	High	⁹Xlow	Xlow	Xlow	Xlow	Xlow	High
MspI	⁴+	+	+	-	-	-,n	-	-	-,n	-
HpaII	+	⁶-,⁸n	-	-	-	-,⁸N	-	-	-,n	-
²MH pattern	⁵(+,+)	(+, -)	(+, -)	⁷(-, -)	(-, -)	(-, -)	(-, -)	(-, -)	(-, -)	(-, -)

¹Frequency of theoretical methylated forms is estimated for plant genomes [16, 37].
²MSAP profile pattern of a fragment with the site after digestion with MspI (M) and HpaII (H).
³(^mC) represents 5-methylcytosine residue.
⁴(+) sequence is cut.
⁵(+) a band is present.
⁶(-) sequence is not cut.
⁷(-) a band is absent.
⁸n and N denote negligible and slow nicking of non-methylated strand, respectively.
⁹Xlow denotes extremely low.

ISSN: 2730-6844