MRE-seq
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The paper "Conserved role of intragenic DNA methylation in regulating alternative promoters" published by Maunakea et al., 2010 is cited for MRE-seq.
MRE is the abbreviation for methyl-sensitive restriction enzyme and these enzymes play a role in the analysis of methylated DNA; they are not able to cleave methylated-cytosine residues, leaving methylated DNA intact. MRE-seq involves sequencing size-selected (100-300 bp) fragments from parallel DNA digestions with these particular MREs: HapII, Hin6I, and AciI.
| Restriction enzyme | Recognition site | Cut |
| HpaII | 5' CCGG
3' GGCC |
5' ---C CGG--- 3'
3' ---GGC C--- 5' |
| Hin6I | 5' GCGC
3' CGCG |
5' ---G CGC--- 3'
3' ---CGC G--- 5' |
| AciI | 5' CCGC
3' GGCG |
5' ---C CGC--- 3'
3' ---GGC G--- 5' |
Supplementary Figure 1 from Maunakea et al. has a nice summary of MRE-seq and MeDIP-seq. From Figure S1, they show MRE-seq reads around the promoter of the PANX2 gene. Below I've obtained the genomic sequence of this region:
>hg19_dna range=chr22:50607707-50609778 5'pad=0 3'pad=0 strand=+ repeatMasking=none CCTGGTTTGCTCACAGCAGTGGCCGGGCCTGTGAACACGGGCTCAAAATACATTTTTGGAATGAATTATTGAATGAACTTAAAACTCCAATCACACTAAA TCTTTTATATGAAAGATCGTGCACGTTCGTCCTGGTATAGTGGGAAGGGGACCTGCACGAGGGAAAACGGCTGCCTCGAAGAGGCAGGGACCACGCGGGA TGCGCCCGCGTCTGAAGCCAGACCCCCGGCTCCCCGAGGGAGAACAGGACGGAGGGCGGGGCTGTGGGGAGCGGAGGGAATGAAGGTCAGGGAGGCGGCG GGGACCCCCTGAGCTGGCACAGGCCCCGGGAACGTCTGTGGAACAGGGGACGGGATGGGGCGTGGGGGAAGGAGGTGCGGGCTGCAGGAGCGGGGGTGAT GGGGTCACTCACGGCGGCGGGACTGGGGGTACTGGGTGGGGGGGTCGGGTGGGGCCGGGGCTGCAGTGGAGGGTGTGGGGCGGGGAGATGCCCTCATTGC CCGCGCACTGGCGCCCGAGCCCAGAGAAGAGAGCGCCGGCTTCCCCGCCAGTGGCCGCAGCACCCCAGGAGCGCGGGAACCTCCGGACCCACAGCGGGGC GCGGCCGGGGCAGGTGGGGGGCCCAGGCGAGGAAGCCCCCTCTGCGCCCTGGGCTGGGCGAAGGGCCCTGCGATGCGACGGGGGCAGCCCCAGCGCGCGC CCAGTCCTCACGTCGCCACCGAGCGGCGCCCCCGCCCCAGCCCGGAGCCCCGCAGGGCCGCCCCCACCCCTGCCCACCCTCCCGCGGGCCGGGGCAGCCC CCCGCCAGCCACCCCGCGTTCCCAGGAAGAGGGACCGGTCATTACTCATTCATGTCCTTTCATTTCATTTCAATATTTTCTGCAAAGTCATCGCCCGCGC CGCATCTGCGTGGCGGGGGGCGGGGTGGGGCGGAGCCACGCCGCGGAGTCGCCGCAGGTAAACAGCCCCCTCCCCGCGGCGGGAGCGGGGCCGCCGGCCC CAGGCAGGGACAGCAGCCGCCGCCCGCGCTCCGGGCCGGGATCCCGCCGCCGCCCCCGCCGGAGGCACGCGCCAGGGCGGGGGCCGGGCTGCGGCGGAGG CGGGCGGCTCCGGTGCCCCCCGCCGCCGCCCCGGCCCGGCCCGCCCGCCCCCTGACCCCGGGGGCGGCGGCGGAGCGCCCCCCAAACCCCGCTGCGGGCT CCGCGCCCGGCCAGCCCCGCACCCGCCGCGCGCCTCCGGCTACTCCCATCCCCCGGAGCCCCCCGCTCGGTCCCGGCGTCCCCTGCCACCCTCTCCCGCG GCCCGCGGCCCCGTCCCCGTCCCGCGCCCCCACGCTCCCCGATCCCCGCCCCCGCGCCGCGCGTCCCCTCCCGCCCGCGCCCCCCTCGCCGGGCCCCGCC CCGCGCCCCCCGCCCCGCCCGCGCCCCCCGCCGGGCCGCGCCCCCCGCCCCCCATGCACCACCTCCTGGAGCAGTCGGCGGACATGGCGACCGCGCTGCT GGCGGGAGAGAAGCTGCGGGAGCTGATCCTGCCGGGCGCGCAGGACGACAAGGCGGGCGCGCTGGCCGCGCTGCTTCTGCAGCTGAAGCTGGAGCTGCCG TTCGACCGGGTGGTCACCATCGGCACCGTGCTGGTGCCCATCCTGCTGGTCACCCTGGTCTTCACCAAGAACTTCGCAGGTGAGGCCGGCGGCCGGGGCG CGGGGCGCGGGCAGAGGGGGCGTCCGCAGGTGTCCGGGAGCTGGCGCTTCCCGCGTCCCCGGCGGCTCCGTCCAGCCGCGCCCACCGTGGCCTGGCTGCG TCCGCGGCGTCCCAGGCACCTTCCACAGCCGCCCCCATCCTAGCAGGTGTCGCTGGTCGCACAGACCCCTCGTCTCTATTTTATTGTTGTTCTTCCTTCC ATTCGTCCGCCCATGGCCGCGGGTGGGACTAGGCCTGTCTGGACCCAGGGGTCCCAAATGTCATGAGACACGGGGTCTGGTTTGGAGAATGTCACAAGCA GCGCCTGAGGGGATGCAGGGTGGCCAGGTGGGGACCAGGAAAGGCCGGGATGGGTGTTGACAGCAGAGAGCT
We can use this tool http://www.restrictionmapper.org/ to do a virtual restriction digest; select the three restriction enzymes (use control to select more than one), and click virtual digest:
My digest
Enzymes: AccI, Hin6I, HpaII
Length 5' Enzyme 5' Base 3' Enzyme 3' Base Sequence
223 Hin6I 1779 Hin6I 2001 CGCCCACCGT GGCCTGGCTG CGTCCGCGGC GTCCCAGGCA CCTTCCACAG
CCGCCCCCAT CCTAGCAGGT GTCGCTGGTC GCACAGACCC CTCGTCTCTA
TTTTATTGTT GTTCTTCCTT CCATTCGTCC GCCCATGGCC GCGGGTGGGA
CTAGGCCTGT CTGGACCCAG GGGTCCCAAA TGTCATGAGA CACGGGGTCT
GGTTTGGAGA ATGTCACAAG CAG
179 HpaII 24 Hin6I 202 CGGGCCTGTG AACACGGGCT CAAAATACAT TTTTGGAATG AATTATTGAA
TGAACTTAAA ACTCCAATCA CACTAAATCT TTTATATGAA AGATCGTGCA
CGTTCGTCCT GGTATAGTGG GAAGGGGACC TGCACGAGGG AAAACGGCTG
CCTCGAAGAG GCAGGGACCA CGCGGGATG
129 HpaII 327 HpaII 455 CGGGAACGTC TGTGGAACAG GGGACGGGAT GGGGCGTGGG GGAAGGAGGT
GCGGGCTGCA GGAGCGGGGG TGATGGGGTC ACTCACGGCG GCGGGACTGG
GGGTACTGGG TGGGGGGGTC GGGTGGGGC
100 HpaII 227 HpaII 326 CGGCTCCCCG AGGGAGAACA GGACGGAGGG CGGGGCTGTG GGGAGCGGAG
GGAATGAAGG TCAGGGAGGC GGCGGGGACC CCCTGAGCTG GCACAGGCCC
97 Hin6I 898 HpaII 994 CGCCGCATCT GCGTGGCGGG GGGCGGGGTG GGGCGGAGCC ACGCCGCGGA
GTCGCCGCAG GTAAACAGCC CCCTCCCCGC GGCGGGAGCG GGGCCGC
80 HpaII 1607 HpaII 1686 CGGGTGGTCA CCATCGGCAC CGTGCTGGTG CCCATCCTGC TGGTCACCCT
GGTCTTCACC AAGAACTTCG CAGGTGAGGC
62 HpaII 836 Hin6I 897 CGGTCATTAC TCATTCATGT CCTTTCATTT CATTTCAATA TTTTCTGCAA
AGTCATCGCC CG
55 Hin6I 1439 Hin6I 1493 CGCCCCCCGC CCCCCATGCA CCACCTCCTG GAGCAGTCGG CGGACATGGC
GACCG
51 HpaII 1274 Hin6I 1324 CGGCGTCCCC TGCCACCCTC TCCCGCGGCC CGCGGCCCCG TCCCCGTCCC
G
51 Hin6I 645 Hin6I 695 CGCCCTGGGC TGGGCGAAGG GCCCTGCGAT GCGACGGGGG CAGCCCCAGC
G
49 Hin6I 645 Hin6I 693 CGCCCTGGGC TGGGCGAAGG GCCCTGCGAT GCGACGGGGG CAGCCCCAG
48 HpaII 456 Hin6I 503 CGGGGCTGCA GTGGAGGGTG TGGGGCGGGG AGATGCCCTC ATTGCCCG
47 HpaII 743 HpaII 789 CGGAGCCCCG CAGGGCCGCC CCCACCCCTG CCCACCCTCC CGCGGGC
46 HpaII 790 HpaII 835 CGGGGCAGCC CCCCGCCAGC CACCCCGCGT TCCCAGGAAG AGGGAC
44 Hin6I 2002 HpaII 2045 CGCCTGAGGG GATGCAGGGT GGCCAGGTGG GGACCAGGAA AGGC
39 HpaII 606 Hin6I 644 CGGGGCAGGT GGGGGGCCCA GGCGAGGAAG CCCCCTCTG
39 Hin6I 1494 HpaII 1532 CGCTGCTGGC GGGAGAGAAG CTGCGGGAGC TGATCCTGC
38 Hin6I 1569 HpaII 1606 CGCTGCTTCT GCAGCTGAAG CTGGAGCTGC CGTTCGAC
35 HpaII 537 Hin6I 571 CGGCTTCCCC GCCAGTGGCC GCAGCACCCC AGGAG
32 HpaII 995 Hin6I 1026 CGGCCCCAGG CAGGGACAGC AGCCGCCGCC CG
30 Hin6I 1325 Hin6I 1354 CGCCCCCACG CTCCCCGATC CCCGCCCCCG
29 Hin6I 698 Hin6I 726 CGCCCAGTCC TCACGTCGCC ACCGAGCGG
29 Hin6I 1706 HpaII 1734 CGCGGGCAGA GGGGGCGTCC GCAGGTGTC
28 Hin6I 1176 Hin6I 1203 CGCCCCCCAA ACCCCGCTGC GGGCTCCG
27 HpaII 2046 none 2072 CGGGATGGGT GTTGACAGCA GAGAGCT
26 HpaII 1085 HpaII 1110 CGGGCTGCGG CGGAGGCGGG CGGCTC
24 Hin6I 203 HpaII 226 CGCCCGCGTC TGAAGCCAGA CCCC
23 none 1 HpaII 23 CCTGGTTTGC TCACAGCAGT GGC
23 HpaII 1037 HpaII 1059 CGGGATCCCG CCGCCGCCCC CGC
23 HpaII 1208 Hin6I 1230 CGGCCAGCCC CGCACCCGCC GCG
22 Hin6I 512 Hin6I 533 CGCCCGAGCC CAGAGAAGAG AG
22 HpaII 1137 HpaII 1158 CGGCCCGCCC GCCCCCTGAC CC
21 HpaII 1111 HpaII 1131 CGGTGCCCCC CGCCGCCGCC C
21 HpaII 1208 Hin6I 1228 CGGCCAGCCC CGCACCCGCC G
21 Hin6I 1539 Hin6I 1559 CGCAGGACGA CAAGGCGGGC G
20 HpaII 1254 HpaII 1273 CGGAGCCCCC CGCTCGGTCC
19 Hin6I 1539 Hin6I 1557 CGCAGGACGA CAAGGCGGG
19 HpaII 1760 Hin6I 1778 CGGCGGCTCC GTCCAGCCG
18 Hin6I 1360 Hin6I 1377 CGCGTCCCCT CCCGCCCG
18 Hin6I 1404 Hin6I 1421 CGCCCCCCGC CCCGCCCG
17 HpaII 1159 Hin6I 1175 CGGGGGCGGC GGCGGAG
17 HpaII 1237 HpaII 1253 CGGCTACTCC CATCCCC
16 HpaII 584 Hin6I 599 CGGACCCACA GCGGGG
16 Hin6I 727 HpaII 742 CGCCCCCGCC CCAGCC
15 Hin6I 1070 HpaII 1084 CGCCAGGGCG GGGGC
15 Hin6I 1745 HpaII 1759 CGCTTCCCGC GTCCC
14 HpaII 1390 Hin6I 1403 CGGGCCCCGC CCCG
12 Hin6I 572 HpaII 583 CGCGGGAACC TC
12 Hin6I 1378 HpaII 1389 CGCCCCCCTC GC
10 HpaII 1060 Hin6I 1069 CGGAGGCACG
10 Hin6I 1422 HpaII 1431 CGCCCCCCGC
10 HpaII 1735 Hin6I 1744 CGGGAGCTGG
9 Hin6I 1560 Hin6I 1568 CGCTGGCCG
8 Hin6I 504 Hin6I 511 CGCACTGG
7 HpaII 1432 Hin6I 1438 CGGGCCG
7 HpaII 1687 HpaII 1693 CGGCGGC
7 Hin6I 1699 Hin6I 1705 CGCGGGG
6 Hin6I 600 HpaII 605 CGCGGC
6 Hin6I 1231 HpaII 1236 CGCCTC
6 HpaII 1533 Hin6I 1538 CGGGCG
5 Hin6I 1027 HpaII 1031 CGCTC
5 HpaII 1032 HpaII 1036 CGGGC
5 HpaII 1132 HpaII 1136 CGGCC
5 Hin6I 1355 Hin6I 1359 CGCCG
5 HpaII 1694 Hin6I 1698 CGGGG
4 Hin6I 1204 HpaII 1207 CGCC
4 HpaII 1533 Hin6I 1536 CGGG
4 Hin6I 694 Hin6I 697 CGCG
3 Hin6I 534 HpaII 536 CGC
2 Hin6I 694 Hin6I 695 CG
2 Hin6I 696 Hin6I 697 CG
2 Hin6I 1229 Hin6I 1230 CG
2 Hin6I 1537 Hin6I 1538 CG
2 Hin6I 1558 Hin6I 1559 CG
There are many fragments in the restriction digestion, which are reflected in the sequenced reads.