. 2014 Jun 19;3(2):426–451. doi: 10.3390/biology3020426

Table 1.

Associations between myogenic differentially methylated regions (DMRs) and overlapping chromatin state for four genes ^a.

Location of Myogenic Differential Methylation	MbMt DMR	Muscle DMR	Gene Product	Previous Relationship to Muscle?	Txn in Mb	Type of Chromatin at the Mb DMR	Figure (Region #)
Hypermethylated DMRs
MARVELD2 , promoter, exon 1, intron 1 chr5:68710817-68711681	yes	yes	epithelial membrane protein	no	little or none	txn elongn	Figure 2, Figure S1 & Figure S2
TBX15 intron 1	yes	yes	T-box txn factor; directs devel. fates	only from txn	strong	weak txn	Figure 4 (1)
chr1:119522311-119522976	yes	yes				weak txn	Figure 4 (1)
TBX15 intron 1	yes	no				txn elongn	Figure 4 (2)
chr1:119526030-119527882	yes	no				txn elongn	Figure 4 (2)
TBX15 Mb promoter	yes	no				low signal	Figure 4 (3)
chr1:119531075-119533079	yes	no				low signal	Figure 4 (3)
TBX15 upstream	yes	yes				low signal	Figure 4 (4)
chr1:119535724-119537175	yes	yes				low signal	Figure 4 (4)
TBX15 upstream	yes	yes				weak txn & weak enhancer	Figure 4 (5)
chr1:119542040-119543970	yes	yes				weak txn & weak enhancer	Figure 4 (5)
TBX15 upstream	yes	yes				weak enhancer	Figure 4 (6)
chr1:119544699-119544773	yes	yes				weak enhancer	Figure 4 (6)
TBX15 upstream	yes	yes				PcG-repressed	Figure 4 (7)
chr1:119549291-119551164	yes	yes				PcG-repressed	Figure 4 (7)
Hypomethylated DMRs
TEAD4 intron2	no	yes	txn factor binding the M-CAT element in promoters or enhancer of muscle genes	yes	strong	weak enhancer	Figure 5 (1)
chr12:3073292-3073324	no	yes				weak enhancer	Figure 5 (1)
TEAD4 intron2	no	yes				txn transition	Figure 5 (2)
chr12:3082851-3082995	no	yes				txn transition	Figure 5 (2)
TEAD4 5' end of intron 3	yes	no				strong enhancer	Figure S6 (3)
chr12:3108155-3108180	yes	no				strong enhancer	Figure S6 (3)
TEAD4 3' end of intron 3	yes	yes				txn elongn	Figure 7 (4)
chr12:3119130-3119880	yes	yes				txn elongn	Figure 7 (4)
TEAD4 intron 5	yes	yes				strong enhancer	Figure 6 (5)
chr12:3123399-3123468	yes	yes				strong enhancer	Figure 6 (5)
TEAD4 exon 7	1 DM site	yes				txn elongn	Figure S7 (6)
chr12:3127664-3127741	1 DM site	yes				txn elongn	Figure S7 (6)
TEAD4 intron 10	yes	yes				strong enhancer	Figure S5 (7)
chr12:3141923-3142819	yes	yes				strong enhancer	Figure S5 (7)
LSP1 lymphoid extended promoter, exon 1, intron 1 (muscle only)	no	yes	F-actin binding	no	strong	weak enhancer & weak txn	Figure 8 (1)
chr11:1875260-1876267	no	yes				weak enhancer & weak txn	Figure 8 (1)
LSP1 Mb extended promoter	yes	yes				weak promoter, strong promoter & strong enhancer	Figure 8 (2)
chr11:1888801-1896175	yes	yes				weak promoter, strong promoter & strong enhancer	Figure 8 (2)
LSP1 last intron	yes	yes				strong enhancer	Figure 8 (3)
chr11:1912289-1912705	yes	yes				strong enhancer	Figure 8 (3)

^a Chromatin states are from ENCODE/Chromatin state segmentation analysis. Txn, transcription; devel., developmental. The regions overlapping low signal had the designation in the ENCODE database of heterochromatin (H3K9me3) or low signal but inspection of the ENCODE/Histone modifications dataset revealed that they did not contain H3K9me3 or H3K27me3 so they are identified as “low signal” chromatin segments in this table.