Mei et al.
Supplementary Figures and Tables
Figure S1 Phylogenetic analysis of NF-YC subfamily
Figure S2 Maize NF-YC family multiple sequence alignments
Figure S3 Sequence for CAPS analysis of NF-YC8
Figure S4 Sequence for methylation analysis of NF-YC8 5’ upstream region
Figure S5 Sequence for methylation analysis of NF-YC8 coding region
Figure S6 Sequence for methylation analysis of Mez1
Figure S7 Bisulfite sequencing for the DMR of Mez1 5’ upstream region
Figure S8 Methylation analysis of the NF-YC8 5’ upstream region
Figure S9 Methylation analysis of the NF-YC8 coding region
Table S1 Methylated cytosine statistics of NF-YC8 in different alleles
Table S2 Sequences of all PCR primers used
Table S3 IDs for Arabidopsis thaliana NF-YC subfamily
Mei et al.
Figure S1 Phylogenetic analysis of NF-YC subfamily. Multiple sequence alignments were generated using
ClustalX 1.83 on full-length proteins as implanted by MEGA 5.0 (Tamura et al. 2011; Thompson et al. 1997).
Phylogenetic trees were constructed by neighbor joining (N-J) with the Possion correction and Pairwise
deletion. Reliability values at each branch point represent the bootstraps cores (1,000 replicates) (Lin et al.
Mei et al.
2011). Sequence of the mouse NF-YC subunit was used to root the tree. The functional annotation of
Arabidopsis thaliana NF-YC was based on Petroni et al. (Petroni et al. 2012). (A) Phylogenetic tree of
maize NF-YC subfamily. (B) Phylogenetic tree of maize and Arabidopsis thaliana NF-YC subfamily.
Figure S2 Maize NF-YC family multiple sequence alignments. The secondary structures, alpha-helix (solid
red cylinders) and coils (black lines), were represented on top of the amino acids sequence, predicted by
PredictProtein and based on Liang et al. (Liang et al. 2014). The DNA-binding consisted of two amino acid
AR and interaction domains were represented by black line. The region of dark blue outline shared with the
structure of H2A (Liang et al. 2014).
Mei et al.
A
B73
ACCAGGACCGACATTTACGACTTCTTGGTCGACATTGTTCCCAGGGATGAGATGAAGGACGACGGAATCGGGCTTCCTAG
Mo17
ACCAGGACCGACATTTACGACTTCTTGGTCGACATTGTTCCCAGGGATGAGATGAAGGACGACGGAATCGGGCTTCCTAG
Consensus
accaggaccgacatttacgacttcttggtcgacattgttcccagggatgagatgaaggacgacggaatcgggcttcctag
80
80
B73
GCCCGGGCTGCCACCCATGGGAGCCCCAGCTGACGCATATCCATACTACTACATGCCACAGCAGCAGGTGCCTGGTCCTG
Mo17
GCCCGGGCTGCCACCCATGGGAGCCCCAGCTGACGCATATCCATACTACTACATGCCACAGCAGCAGGTGCCTGGTCCTG
Consensus
gcccgggctgccacccatgggagccccagctgacgcatatccatactactacatgccacagcagcaggtgcctggtcctg
160
160
B73
GGATGGTTTATGGCGCCCAGCAAGGCCACCCGGTGACGTATCTGTGGCAGGATCCTCAGGAACAGCAGGAGCAAGCTCCT
Mo17
GGATGGTTTATGGCGCCCAGCAAGGCCACCCGGTGACGTATCTGTGGCAGGATCCTCAGGAACAGCAGGAGCAAGCTCCC
Consensus
ggatggtttatggcgcccagcaaggccacccggtgacgtatctgtggcaggatcctcaggaacagcaggagcaagctcc
240
240
B73
GAAGAGCAGCAGTCTCTGCATGAAAGGGACTGAGGATGTCGCTCA..AGCTATCACCTGATTTTTCAGAGCTCTCATTTT
Mo17
GAAGAGCAGCAGTCTCTGCATGAAAGGGACTGAGGATGTCGCTCAGAAGCTATCACCTGATTTTTCAGAGCTCTCATTTT
Consensus
gaagagcagcagtctctgcatgaaagggactgaggatgtcgctca agctatcacctgatttttcagagctctcatttt
318
320
B73
AGGTTCTCTAAACTGCAGGTTTTCGTTGGCTAATATCGTTGGGTATCAAACTGAAACAGGTAGGGTGTAGCATCATGGTA
Mo17
AGGTTGTCTAAACTGCAGGTTTTCGTTGGCTAATATCGTTGGGTATCAAACTGAAACAGGTAGGGTGTAGCATCATGGTA
Consensus
aggtt tctaaactgcaggttttcgttggctaatatcgttgggtatcaaactgaaacaggtagggtgtagcatcatggta
398
400
B73
GTTTGATTTCTGCTGTGGTGTTAGTTGGAGGGATAATGATTAGCGGCTAGTGGATTAAAGTTACCCATACCGTT
Mo17
GTTTGATTTCTGCTGTGGTGTTAGTTGGAAGGATAATGATTAGCGGCTAGTGGATTAAAGTTACCCATACCGTT
Consensus
gtttgatttctgctgtggtgttagttgga ggataatgattagcggctagtggattaaagttacccataccgtt
472
474
Mei et al.
B
HuangC
AGATCTCCTGCACCTTCGAACTCTGGAAAGATCATAGATTTTTGGGCAATAGTAAGTGGACATGGAACCATCCTCTCAGC
178
AGATCTCCTGCACCTTCGAACTCTGGAAAGATCATAGATTTTTGGGCAATAGTAAGTGGACATGGAACCATCCTCTCAGC
Consensusagatctcctgcaccttcgaactctggaaagatcatagatttttgggcaatagtaagtggacatggaaccatcctctcagc
80
80
HuangC
CTCAGCCTGCGATGGGTGTCGCCGCCGGTGGGTCACAAGTGTATCCTGCCTCTGCCTACCCGCCTGCAGCAACAGTAGCT
178
CTCAGCCTGCGATGGGTGTCGCCGCCGGTGGGTCACAAGTGTATCCTGCCTCTGCCTACCCGCCTGCAGCAACAGTAGCT
Consensusctcagcctgcgatgggtgtcgccgccggtgggtcacaagtgtatcctgcctctgcctacccgcctgcagcaacagtagct
160
160
HuangC
CCTCCTGCTGTTGCATCTGCTGGTTTACAGTCAGTGCAACCATTCCCAGCCAACCCTGCCCATATGAGTGCTCAGCACCA
178
CCTCCTGCTGTTGCATCTGCTGGTTTACAGTCAGTGCAACCATTCCCAGCCAACCCTGCCCATATGAGTGCTCAGCACCA
Consensuscctcctgctgttgcatctgctggtttacagtcagtgcaaccattcccagccaaccctgcccatatgagtgctcagcacca
240
240
HuangC
GATTGTCTACCAACAAGCTCAACAGTTCCACCAACAGCTCCAGCAGCAGCAACAGCAGCAGCTTCAGCAGTTCTGGGTCG
178
GATTGTCTACCAACAAGCTCAACAGTTCCACCAACAGCTCCAGCAGCAGCAACAGCAGCAGCTTCAGCAGTTCTGGGTCG
Consensusgattgtctaccaacaagctcaacagttccaccaacagctccagcagcagcaacagcagcagcttcagcagttctgggtcg
320
320
HuangC
AACGCATGACTGAAATCGAGGCAACAGCTGATTTCAGGAACCACAACTTGCCACTTGCGAGGATAAAGAAGATCATGAAG
178
AACGCATGACTGAAATCGAGGCAACAGCTGATTTCAGGAACCACAACTTGCCACTTGCGAGGATAAAGAAGATCATGAAG
Consensusaacgcatgactgaaatcgaggcaacagctgatttcaggaaccacaacttgccacttgcgaggataaagaagatcatgaag
400
400
HuangC
GCCGACGAAGATGTCCGCATGATCTCAGCCGAAGCTCCCGTGGTCTTCGCAAAAGCTTGCGAGATATTCATACTGGAGCT
178
GCCGACGAAGATGTCCGCATGATCTCAGCCGAAGCTCCCGTGGTCTTCGCAAAAGCTTGCGAGATATTCATACTAGAGCT
Consensusgccgacgaagatgtccgcatgatctcagccgaagctcccgtggtcttcgcaaaagcttgcgagatattcatact gagct
480
480
HuangC
GACGCTGAGGTCGTGGATGCACACCGAGGAGAACAAGCGCCGCACCTTGCAGAAGAACGACATTGCCGCAGCCATCACCA
178
GACGCTGAGGTCGTGGATGCACACCGAGGAGAACAAGCGCCGCACCTTGCAGAAGAACGACATTGCCGCAGCCATCACCA
Consensusgacgctgaggtcgtggatgcacaccgaggagaacaagcgccgcaccttgcagaagaacgacattgccgcagccatcacca
560
560
HuangC
GGACCGACATTTACGACTTCTTGGTCGACATTGTTCCCAGGGATGAGATGAAGGACGACGGAATCGGGCTTCCTAGGCCC
178
GGACCGACATTTACGACTTCTTGGTCGACATTGTTCCCAGGGATGAGATGAAGGACGACGGAATCGGGCTTCCTAGGCCC
Consensusggaccgacatttacgacttcttggtcgacattgttcccagggatgagatgaaggacgacggaatcgggcttcctaggccc
640
640
HuangC
GGGCTGCCACCCATGGGAGCCCCAGCTGACGCATATCCATACTACTACATGCCACAGCAGCAGGTGCCTGGTCCTGGGAT
178
GGGCTGCCACCCATGGGAGCCCCAGCTGACGCATATCCATACTACTACATGCCACAGCAGCAGGTGCCTGGTCCTGGGAT
Consensusgggctgccacccatgggagccccagctgacgcatatccatactactacatgccacagcagcaggtgcctggtcctgggat
720
720
HuangC
GGTTTATGGCGCCCAGCAAGGCCACCCCGTGACGTATCTGTGGCAGGATCCTCAGGAACAGCAGGAGCAAGCTCCCGAAG
178
GGTTTATGGCGCCCAGCAAGGCCACCCCGTGACGTATCTGTGGCAGGATCCTCAGGAACAGCAGGAGCAAGCTCCCGAAG
Consensusggtttatggcgcccagcaaggccaccccgtgacgtatctgtggcaggatcctcaggaacagcaggagcaagctcccgaag
800
800
HuangC
AGCAGCAGTCTCTGCATGAAAGGGACTGAGGATGTCGCACGTG
178
AGCAGCAGTCTCTGCATGAAAGGGACTGAGGATGTCGCACGTG
Consensusagcagcagtctctgcatgaaagggactgaggatgtcgcacgtg
843
843
Figure S3 Sequence for CAPS analysis of NF-YC8. (A) Sequence for CAPS analysis of NF-YC8 in B73 and
Mo17. This region contains a part of 3’ untranslated region. The SNP site was marked by red outline. (B)
Sequence for CAPS analysis of NF-YC8 in Huang C and 178. The SNP site was marked by red outline.
Mei et al.
B73
CCCTTAGAGTTGATATAGCTCACTGACTTTTCAGCCTGTTCTTTTTACTGAAGAGCCATTGGCAATTTTGCCATTATCAT
Mo17
CCTTTAGAGTTGATATAGCTCACTGACTTTTCAGCCTGTTCTTCTT..................................
Consensus
cc ttagagttgatatagctcactgacttttcagcctgttctt tt
203
169
B73
TTGTGGGCTTCGCCAGTATGCCATCGGACCCACAAATCATAGACACAGACGGTCCCACCAGTCATAGACACGGGATGGCA
Mo17
................................................................................
Consensus
283
169
B73
TAATAACAAACAGCCAAAATTGAGAGTGGCAAAATAGCAAATTTCTCTTTTACTGAATGAGCAGGAGTGACGACAGGCTA
Mo17
................................................TTTACTGAATGAGCAGGAGTGACGACAGGCTA
Consensus
tttactgaatgagcaggagtgacgacaggcta
363
201
B73
CAGTTTCGGTCAGTGTCATCGGAGTCGGACGACAACCACGCGTACGTCCGCGACAAGGGCGATGACATGGTCGCAAGGTG
Mo17
CAGTTTCGGTCAGTGTCATCGGAGTCGGACGACAACCACGCGTACGTCCGCGACAAGGGCGATGACATGGTCGCAAGGTG
Consensus
cagtttcggtcagtgtcatcggagtcggacgacaaccacgcgtacgtccgcgacaagggcgatgacatggtcgcaaggtg
443
281
B73
AAATTGAAGCCCGGCCTCATGGGCTGCGTCATGTGTGCATTTGCTGTGCTCGATTACTCGGAGGAGCATTTGCTTGCTTC
Mo17
AAATTGAAGCCCGGCCTCATGGGCTGCGTCATGTGTGCATTTGCTGTGCTCGATTACTCGGAGGAGCATTTGCTTGCTTC
Consensus
aaattgaagcccggcctcatgggctgcgtcatgtgtgcatttgctgtgctcgattactcggaggagcatttgcttgcttc
523
361
B73
GTCCTTATCCTCCTTCCAAGACCAACCCTCGTATGCACGGTGACGTTAGCGCTAGGCTCTATTTGGAAGATGACTGATTC
Mo17
GTCCTTATCCTCCTTCCAAGACCAACCCTCGTATGCACGGTGACGTTAGCGCTAGGCTCTATTTGGAAGATGACTGATTC
Consensus
gtccttatcctccttccaagaccaaccctcgtatgcacggtgacgttagcgctaggctctatttggaagatgactgattc
603
441
B73
TTGGTTTTTAAGGAACCGAGAAATCAGTTTTTAGAAATTGAATAAAAAAATTGACATATTTAGAGATCTTCCGGCTTTTA
Mo17
TTGGTTTTTAAGGAACCGAGAAATCAGTTTTTAGAAATTGAATAAAAAA.TTGACATATTTAGAGATCTTCCGGCTTTTA
Consensus
ttggtttttaaggaaccgagaaatcagtttttagaaattgaataaaaaa ttgacatatttagagatcttccggctttta
683
520
B73
AAAACCAGTTTTCAAGAAACTAGATGTATCCAAACAAGTCTTAGACTATCTCCAGCAACGTCCTCTATATACATTATCTA
Mo17
AAAACCAGTTTTCAAGAAACTAGATGTATCCAAACAAGTCTTAG....................................
Consensus
aaaaccagttttcaagaaactagatgtatccaaacaagtcttag
763
564
B73
TATCCGTCTTTTACAGTCTCCTCTAAAAGATTTCATCTCCTATATCTACTTTCTCTTCAACAACGTCCTCTAAATCACGT
Mo17
................................................................................
Consensus
843
564
B73
CCTCTATATGTAAATACCTATATTAAAGACATTTTTAATTTTTTTAATTTTTGTACATACGTATTTGTCATACTCTCAAA
Mo17
................................................................................
Consensus
923
564
B73
TGTATTTTACATATTTTAGTTTTATTAAACCGGTTTAATAATAGATAGAGAACCGTTTAGAGAAACTCTACATATAGAGG
Mo17
................................................................................
Consensus
1003
564
B73
ATTCAGCAACGTTCTCTAAATTTAGAGGACCGTTTAGAGGACGTTGCTGGAGGGAGTAAAGGACGTCCTCGTCCTCTAAA
Mo17
................................................................................
Consensus
1083
564
B73
TTTAGGGTACAGGATCCTTTAGAGGGTCTTGTTGGAGCCAGCCTTAGTAGAGCTGCCCCTAGATTTTAAACTCACTTTTT
Mo17
...............................................TAGAGCTGCCCCTAGATTTTAAACTCACTTTTT
Consensus
tagagctgcccctagattttaaactcacttttt
1163
597
B73
AGGTTGCAAGGCAGTCATTTGCACAACCACGGTCCGTTTCCATGGCGACCCGCTCTCTGCCACCGACGCCCGGGCCCGCG
Mo17
AGGTTGCAAGGCAGTCATTTGCACAACCACGGTCCGTTTCCATGGCGACCCGCTCTCTGCCACCGACGCCCGGGCCCGCG
Consensus
aggttgcaaggcagtcatttgcacaaccacggtccgtttccatggcgacccgctctctgccaccgacgcccgggcccgcg
1243
677
B73
GCCCAAACACCACCTGGACGGCTTGGGCCCCAGTACGGACCGGATTGAGGCCTGGCCTGGACCCGGAAGCACCAGGTGGT
Mo17
GCCCAAACACCACCTGGACGGCTTGGGCCCCAGTACGGACCGGATTGAGGCCTGGCCTGGACCCGGAAGCACCAGGTGGT
Consensus
gcccaaacaccacctggacggcttgggccccagtacggaccggattgaggcctggcctggacccggaagcaccaggtggt
1323
757
B73
GCTGCCAATGGGACGCACGCTTTCGCTCCGAGGAGAATTTAAGAACCGAGTAGGCAGACAGGGAAGGCTAGGAGGGGACT
Mo17
GCTGCCAATGGGACGCACGCTTTCGCTCCGAGGAGAATTTAAGAACCGAGTAGGCAGACAGGGAAGGCTAGGAGGGGACT
Consensus
gctgccaatgggacgcacgctttcgctccgaggagaatttaagaaccgagtaggcagacagggaaggctaggaggggact
1403
837
B73
AGGGGAGAGAGAGAG........GGGGAAGGCCAA
Mo17
AGGGGAGAGAGAGAGAGAGAGAGGGGGAAGGCCAA
Consensus
aggggagagagagag
ggggaaggccaa
1430
872
Figure S4 Sequence for methylation analysis of NF-YC8 5’ upstream region. The simple TE region was
marked by red underline, repeat region was marked by blue underline.
Mei et al.
B73
GGTCACAAGTGTATCCTGCGTCTGCCTACCCGCCTGCAGCAACAGTAGCTCCTCCTGCTGTTGCATCTGCTGGTTTACAG
Mo17
GGTCACAAGTGTATCCTGCCTCTGCCTACCCGCCTGCAGCAACAGTAGCTCCTCCTGCTGTTGCATCTGCTGGTTTACAG
Consensus
ggtcacaagtgtatcctgc tctgcctacccgcctgcagcaacagtagctcctcctgctgttgcatctgctggtttacag
80
80
B73
TCAGTGCAACCATTCCCAGCCAACCCTGCCCATATGAGTGCTCAGCACCAGATTGTCTACCAACAAGCTCAACAGTTCCA
Mo17
TCAGTGCAACCATTCCCAGCCAACCCTGCCCATATGAGTGCTCAGCACCAGATTGTCTACCAACAAGCTCAACAGTTCCA
Consensus
tcagtgcaaccattcccagccaaccctgcccatatgagtgctcagcaccagattgtctaccaacaagctcaacagttcca
160
160
B73
CCAACAGCTCCAGCAGCAGCAACAGCAGCAGCTTCAGCAGTTCTGGGTCGAACGCATGACTGAAATCGAGGCAACAGCTG
Mo17
CCAACAGCTCCAGCAGCAGCAACAGCAGCAGCTTCAGCAGTTCTGGGTCGAACGCATGACTGAAATCGAGGCAACAGCTG
Consensus
ccaacagctccagcagcagcaacagcagcagcttcagcagttctgggtcgaacgcatgactgaaatcgaggcaacagctg
240
240
B73
ATTTCAGGAACCACAACTTGCCACTTGCGAGGATAAAGAAGATCATGAAGGCCGACGAAGATGTCCGCATGATCTCAGCC
Mo17
ATTTCAGGAACCACAACTTGCCACTTGCGAGGATAAAGAAGATCATGAAGGCCGACGAAGATGTCCGCATGATCTCAGCC
Consensus
atttcaggaaccacaacttgccacttgcgaggataaagaagatcatgaaggccgacgaagatgtccgcatgatctcagcc
320
320
B73
GAAGCTCCCGTGGTCTTCGCAAAAGCTTGCGAGATATTCATACTGGAGCTGACGCTGAGGTCGTGGATGCACACCGAGGA
Mo17
GAAGCTCCCGTGGTCTTCGCAAAAGCTTGCGAGATATTCATACTGGAGCTGACGCTGAGGTCGTGGATGCACACCGAGGA
Consensus
gaagctcccgtggtcttcgcaaaagcttgcgagatattcatactggagctgacgctgaggtcgtggatgcacaccgagga
400
400
B73
GAACAAGCGCCGCACCTTGCAGAAGAACGACATTGCCGCAGCCATCACCAGGACCGACATTTACGACTTCTTGGTCGACA
Mo17
GAACAAGCGCCGCACCTTGCAGAAGAACGACATTGCCGCAGCCATCACCAGGACCGACATTTACGACTTCTTGGTCGACA
Consensus
gaacaagcgccgcaccttgcagaagaacgacattgccgcagccatcaccaggaccgacatttacgacttcttggtcgaca
480
480
B73
TTGTTCCCAGGGATGAGATGAAGGACGACGGAATCGGGCTTCCTAGGCCCGGGCTGCCACCCATGGGAGCCCCAGCTGAC
Mo17
TTGTTCCCAGGGATGAGATGAAGGACGACGGAATCGGGCTTCCTAGGCCCGGGCTGCCACCCATGGGAGCCCCAGCTGAC
Consensus
ttgttcccagggatgagatgaaggacgacggaatcgggcttcctaggcccgggctgccacccatgggagccccagctgac
560
560
B73
GCATATCCATACTACTACATGCCACAGCAGCAGGTGCCTGGTCCTGGGATGGTTTATGGCGCCCAGCAAGGCCACCCGGT
Mo17
GCATATCCATACTACTACATGCCACAGCAGCAGGTGCCTGGTCCTGGGATGGTTTATGGCGCCCAGCAAGGCCACCCGGT
Consensus
gcatatccatactactacatgccacagcagcaggtgcctggtcctgggatggtttatggcgcccagcaaggccacccggt
640
640
B73
GACGTATCTGTGGCAGGATCCTCAGGAACAGCAGGAGCAAGCTCCTGAAGAG
Mo17
GACGTATCTGTGGCAGGATCCTCAGGAACAGCAGGAGCAAGCTCCCGAAGAG
Consensus
gacgtatctgtggcaggatcctcaggaacagcaggagcaagctcc gaagag
692
692
Figure S5 Sequence for methylation analysis of NF-YC8 coding region
B73
CTTGGTTTTGACTTTTGATGGGACCGCTTTAAGGAATTATGGGCCTGTTTGAGACAACTTTTTT.GGAAGAACTTTTCTG
Mo17
GATGGCTTGG..TTTTGATGTGACTCCTTTAAGGAATTATGGGCCTGTTTGAGACAATTTTTTTTGAAAGAACTTTTCTG
Consensustgg tt g ttttgatg gac ctttaaggaattatgggcctgtttgagacaa tttttt g aagaacttttctg
79
78
B73
AGAATATGAATTCTTGGATAATATAGCTGTCACGAGAATCTAGATATCACGAGGCTTCTATGCAGAGCAAGATAAAGGGG
Mo17
AGAATATGAATTTTTGGATAATATAACTGTCACGAGAATCTGAATATCACGGGGCTTCTATGCAGAGCAAGTTAAAGGGG
Consensus
agaatatgaatt ttggataatata ctgtcacgagaatct atatcacg ggcttctatgcagagcaag taaagggg
159
158
B73
CATGCACAATTTAGGGTTTAAGAAGCCATAGATTCCTTGCGTCGCAACGACTCGATAAATTCTACATTTACGCGTTGAAT
Mo17
CCTGCACAATTTAGGGTTTAAGAAGCGACAGATTCCTTGCGTCGCAACGACTCGACAAATTCTACATTCACGCGTTGAAT
Consensus
c tgcacaatttagggtttaagaagc a agattccttgcgtcgcaacgactcga aaattctacatt acgcgttgaat
239
238
B73
CAAGCGATTTTCACACATAAAAATGATTCTCACATAAACGGACTGAGAAAAGACGACTAGAATTCAACCAGAAGCCAAAA
Mo17
CGAGTGATTTTCACACA..AAAATGATTCTCACATAAATGGACTGAGAAACGACGACTAGAATTTGACCAGAAGCCGAAA
Consensus
c ag gattttcacaca aaaatgattctcacataaa ggactgagaaa gacgactagaatt accagaagcc aaa
319
316
B73
CAAACAAGGACCATGTTATGTTATGCTACGTTT
Mo17
CAAACAACGACCATGTTATGTTATGTTACACTT
Consensus
caaacaa gaccatgttatgttatg tac tt
352
349
Figure S6 Sequence (DMR) for methylation analysis of Mez1 (Haun et al. 2007)
Mei et al.
Figure S7 Bisulfite sequencing for the DMR of Mez1 5’ upstream region. (A, B) B73xMo17; (C, D)
Mo17xB73. The DMR (350 bp) of the maternally expressed gene Mez1 5’ upstream was employed for
verifying our bisulfite converted DNA templates. The specific-primers were used to amplify the DMR and
the B73/Mo17 sequence polymorphisms allowed exact determination of the parental alleles for each clone.
9-15 bisulfite clones of each fragment were sequenced.
Mei et al.
Figure S8 Methylation analysis of the NF-YC8 5’ upstream region. (A-C) Methylation sites analysis of B73
alleles in endosperm tissues derived from B73xMo17 (maternal) and Mo17xB73 (paternal) reciprocal
crosses at 18 DAP (TE region: -1244--1083; Repeat region: -686--273, differential methylated region was
marked by red outline). (D-F) Methylation sites analysis of Mo17 alleles in endosperm tissues derived from
Mo17xB73 (maternal) and B73xMo17 (paternal) reciprocal crosses at 18 DAP.
Mei et al.
Figure S9 Methylation analysis of the NF-YC8 coding region. (A, B) Methylation sites analysis of B73
alleles in endosperm tissues derived from B73xMo17 (maternal) and Mo17xB73 (paternal) reciprocal
crosses at 18 DAP. (C, D) Methylation sites analysis of Mo17 alleles in endosperm tissues derived from
Mo17xB73 (maternal) and B73xMo17 (paternal) reciprocal crosses at 18 DAP.
Mei et al.
Table S1 Methylated cytosine statistics of NF-YC8 in different alleles
Table S1A Number of methylated cytosine in NF-YC8 5’ upstream of B73 allele
Region 1 (-1287--1081)
Number of
clones
CG (4 sites)
CHG (8 sites)
CHH (35 sites)
B73xMo17_B73 allele
9
32/36 (88.89%)
57/72 (79.17%)
167/315 (53.02%)
Mo17xB73_B73 allele
11
32/44 (72.73%)
83/88 (94.32%)
272/385 (70.65%)
Region 2 (-1082--699)
Number of
clones
CG (23 sites)
CHG (14 sites)
CHH (45 sites)
B73xMo17_B73 allele
8
11/184 (5.98%)
15/112 (13.39%)
18/360 (5%)
Mo17xB73_B73 allele
7
10/161 (6.21%)
14/98 (14.29%)
10/315 (3.17%)
Region 3 (-698--519)
Number of
clones
CG (4 sites)
CHG (3 sites)
CHH (36 sites)
B73xMo17_B73 allele
12
43/48 (89.58%)
23/36 (63.89%)
64/432 (14.81%)
Mo17xB73_B73 allele
14
196/196 (100%)
32/42 (76.19%)
183/504 (36.31%)
Region 4 (-518--241)
Number of
clones
CG (8 sites)
CHG (8 sites)
CHH (31 sites)
B73xMo17_B73 allele
7
51/56 (91.07%)
25/56 (44.64%)
33/217 (15.21%)
Mo17xB73_B73 allele
14
109/112 (97.32%)
41/112 (36.61%)
41/434 (9.44%)
Region 5 (-240-+26)
Number of
clones
CG (18 sites)
CHG (19 sites)
CHH (40 sites)
B73xMo17_B73 allele
11
6/198 (3.03%)
12/209 (5.74%)
32/440 (7.27%)
Mo17xB73_B73 allele
7
0/126 (0%)
3/133 (2.26%)
12/280 (4.29%)
Mei et al.
Table S1B Number of methylated cytosine in NF-YC8 5’ upstream of Mo17 allele
Region 1 (-674--272)
Number of
clones
CG (23 sites)
CHG (15 sites)
CHH (48 sites)
B73xMo17_Mo17 allele
15
21/345 (6.09%)
40/225 (17.78%)
56/720 (7.78%)
Mo17xB73_Mo17 allele
11
12/253 (4.74%)
25/165 (15.15%)
29/528 (5.49%)
Region 2 (-271-+16)
Number of
clones
CG (18 sites)
CHG (19 sites)
CHH (43 sites)
B73xMo17_Mo17 allele
10
6/180 (3.33%)
8/190 (4.21%)
43/430 (10%)
Mo17xB73_Mo17 allele
10
2/180 (1.11%)
9/190 (4.74%)
9/430 (2.09%)
Table S1C Number of methylated cytosine in TE and repeat region of B73 allele
TE region (-1244--1083)
Number of
clones
CG (4 sites)
CHG (5 sites)
CHH (30 sites)
B73xMo17_B73 allele
9
32/36 (88.89%)
40/45 (88.89%)
162/360 (45%)
Mo17xB73_B73 allele
11
32/44 (72.73%)
55/55 (100%)
263/330 (79.70%)
Repeat region (-686--273)
Number of
clones
CG (12 sites)
CHG (10 sites)
CHH (58 sites)
B73xMo17_B73 allele
7
76/84 (90.48%)
36/70 (51.43%)
67/406 (16.5%)
Mo17xB73_B73 allele
14
165/168 (98.21%)
73/140 (52.14%)
196/812 (24.14%)
Mei et al.
Table S1D Number of methylated cytosine of NF-YC8 coding region
Region 1 (+4080-+4421)
Number of
clones
CG (12 sites)
CHG (36 sites)
CHH (58 sites)
B73xMo17_B73 allele
7
76/84 (90.48%)
26/252 (10.32%)
12/406 (2.96%)
Mo17xB73_B73 allele
8
89/96 (92.71%)
37/288 (12.85%)
13/472 (2.75%)
Region 2 (+4422-+4771)
Number of
clones
CG (20 sites)
CHG (28 sites)
CHH (51 sites)
B73xMo17_B73 allele
6
66/120 (55%)
28/168 (16.67%)
12/306 (3.92%)
Mo17xB73_B73 allele
9
130/180 (72.22%)
51/252 (20.24%)
20/459 (4.36%)
Region 1 (+4080-+4421)
Number of
clones
CG (11 sites)
CHG (36 sites)
CHH (60 sites)
B73xMo17_Mo17 allele
5
40/55 (72.73%)
9/180 (5%)
4/300 (1.33%)
Mo17xB73_Mo17 allele
6
60/66 (90.91%)
60/216 (27.78%)
19/360 (5.28%)
Region 2 (+4422-+4771)
Number of
clones
CG (21 sites)
CHG (28 sites)
CHH (51 sites)
B73xMo17_Mo17 allele
7
87/ 147 (59.18%)
29/196 (14.80%)
12/357 (3.36%)
Mo17xB73_Mo17 allele
7
93/147 (63.27%)
32/196 (16.33%)
14/357 (3.92%)
CGG sites are counted as CG sites not as CHG. Asymmetric is defined by cytosine in the context CHH,
where H=A, T, or C. Each fraction represents the number of cytosine methylated out of the total number of
sites analyzed (Hermon et al. 2007).
Mei et al.
Table S2 Sequences of all PCR primers used
Table S2A Primers for clone
NF-YC8 clone
NF-YC8F
NF-YC8R
NF-YC8 RACE
5'GSP-1
5'GSP-2
3'GSP-1
3'GSP-2
NF-YC8 CAPS analysis
CAPS-F
CAPS-R
NF-YC8 RT-PCR
RT-F
RT-R
NF-YC8 Promoter region Pr-F
Pr-R
NF-YC8 Intron region
Fragment1F
Fragment1R
Fragment2F
Fragment2R
Mez1
Mez1F
Mez1R
NF-YC13 RT-PCR
RT-F
RT-R
NF-YC14 RT-PCR
RT-F
RT-R
TGCACCTTCGAACTCTGGAAA
CGACATCCTCAGTCCCTTTCAT
CCACGACCTCAGCGTCAGCTCCAGTAT
CCAGCAGATGCAACAGCAGGAGGAGC
GCTCCTCCTGCTGTTGCATCTGCTGG
ATACTGGAGCTGACGCTGAGGTCGTGG
ACCAGGACCGACATTTACGACTT
AACGGTATGGGTAACTTTAATCCAC
CGCATGACTGAAATCGAGGCAA
AAGTCGTAAATGTCGGTCCTGGT
CCCTTAGAGTTGATATAGCTCACTGACT
CACTTCGAAGGTGCAGCAGAAGGT
CATTCTCCAATCCGTGCCCTAGTC
GTAAGGCCATTGACACATGTCCTC
GAGGACATGTGTCAATGGCCTTAC
GAGGATGGTTCCATGTCCACTTGC
AGGAATCTTGATCCTACATTCTTC
ATAACCTCGAGATAAAACAATCCC
TAGGGCTGGTCTGCCACCCAT
CACCCTACTTAGAATCGCCTGTTT
TGGAGTAGACACGTCGGCTCAA
TAGTCCAGAACTCCCTGAGCTG
Mei et al.
Table S2B Primers for methylation analysis
Bisulfite sequencing for NF-YC8
Promoter region
Bsr1-F1B
Bsr1-R1B
Bsr1-F2B(Second round)
Bsr1-R2B(Second round)
Bsr2-F1B
Bsr2-R1B
Bsr3-F1B
Bsr3-R1B
Bsr4-F1B
Bsr4-R1B
Bsr5-F1B
Bsr5-R1B
Bsr1-F1M
Bsr1-R1M
Bsr1-F2M(Second round)
Bsr2-F1M
Bsr2-R1M
Coding region Bsr6-F1B
Bsr6-F1M
Bsr6-R1
Bsr7-F1
Bsr7-R1B
Bsr7-R1M
Bisulfite sequencing for Mez1
BSr-F1B
BSr-F2B(Second round)
BSr-R1B
BSr-F1M
BSr-F2M(Second round)
BSr-R1M
TTAGAGTTGATATAGTTTAYTGAYTTTTYAGTYTG
CTRTCRTCACTCCTRCTCATTCARTA
GTTGATATAGTTTAYTGAYTTTTYAGTYTGTT
ACCRAAACTRTAACCTRTCRTCAC
TAYTGAATGAGYAGGAGTGAYGAYAG
AACRTTRCTRAAAATAATCTAARACTTRTTTRAAT
ATTYAAAYAAGTYTTAGATTATTTTYAGYAAYGTT
AAATACATTTRAAAATATAACAAATACRTATATAC
GTATATAYGTATTTGTTATATTTTYAAATGTATTT
TAATTRTACAAATAACTRCCTTRCAACCT
AGGTTGYAAGGYAGTTATTTGTAYAATTA
TTRACCTTCCCCCTCTCTCTCTCC
ATGTATTYAAAYAAGTRTTAGTAGAGYTGTT
TCTAAAAACARCTCTACTAARACTTRTTTAAAT
TTAYTGAATGAGYAGGAGTGAYGA
ATTTAAAYAAGTYTTAGTAGAGYTGTTTTTAGA
CCTCTCTCTCTCTCTCTCTCC
GGTTATAAGTGTATTYTGYGTYTGTTTAT
GGTTATAAGTGTATTYTGTTTYTGTTTAT
TATCTCRCAAACTTTTACRAAAACCA
AAGTTTGYGAGATATTTATAYTGGAGTT
CTCTTCARAAACTTACTCCTRCTRTT
CTCTTCRRAAACTTACTCCTRCTRTT
TTATTTTTTYTGTGTTYAAAGGGGGTTA
TTGGTTTTGATTTTTGATGGGA
AAACRTAACATAACATAACATAATCCTT
TTGTTTTTTGYAATTYAAAGGGGGTTAA
GATGGTTTGGTTTTGATGTGA
AAATATAACATAACATAACATAATCRTT
Mei et al.
Table S3 IDs for Arabidopsis thaliana NF-YC subfamily (Siefers et al. 2009)
NF-YC1
NF-YC2
NF-YC3
NF-YC4
NF-YC5
NF-YC6
NF-YC7
NF-YC8
NF-YC9
NF-YC10
NF-YC11
NF-YC12
NF-YC13
The
protein
sequences
of
AT3G48590
AT1G56170
AT1G54830
AT5G63470
AT5G50490
AT5G50480
AT5G50470
AT5G27910
AT1G08970
AT1G07980
AT3G12480
AT5G38140
AT5G43250
Arabidopsis
thaliana
NF-YC
subfamily
were
downloaded
from
http://ensembl.gramene.org/Arabidopsis_thaliana/Info/Index.
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