Sequence name or
accession a /

Putative annotation

and top NRAA hit b /

Primers c

/ Amplified fragment region and length d (bp)

Cinful

/ Gypsy-like retroelement
AF049110 (Zm) repetitive / F gggctcaagaatgctggagg
R agacttcggtcgacttcagc / polyprotein
417 g/c

Huck2

/ Gypsy-like retroelement
AF391808 (Zm) repetitive / F CACAGCTCGAGCAAGTCC
R ATGAGGTTCCGAGGGGTAT / gag/pol
365 g/c

Opie2

/ Copia-like retroelement
U68408 (Zm) repetitive / F agaggaagggatcaagcacg
R tagaccctgttgatggcgtgg / pol
179 g/c

Mu TIR

/ Mutator (Mu) transposon
M76978 (Zm)
repetitive / F GGGATTCGACGAAATGGAGGC
R GCACACAGGAACGGTAAACG / Mu terminal inverted repeat (TIR)
147 g/c

MuDRa

/ Mutator (Mu) transposon
U14597 (Zm) repetitive / F ATCCGGCATTGGGCGAAACA
R TTGTCCGTATCCAAACTTCCCT / MuDRa derivative
transposase
386 g – 241 c

CentC

/ Centromeric satellite
AF078921 (Zm) repetitive / F GGTTCCTGTGCCAAAAACTCG
R CAACGAACATGCCCAATCCAC / centromeric repeat
138 g ladder

CRM2 GAG

/ Centromeric gypsy-like retrotransposon (CRM)
AY129008 repetitive / F gcacttacgaccaaaccgcacc
R gattcggcaaagatgcaccagg / gag 90
625 g/c

CRM2 LTR

/ Centromeric gypsy-like retrotransposon (CRM)
AY129008 repetitive / F gacccgtgcactcttgttttgcttagg
R gctctgattaccaactgatgtgcaccc / long terminal repeat (LTR)
802 g/c

rDNA 5S

/ rDNA 5S
AF242647 (Zm) repetitive / F TGGGAAGTCCTCGTGTTGC
R GTGCTGGTATGATCGCATCC / 5S gene and intergenic spacer
238 g/c

rDNA 26S

/ rDNA 26S
BT018529 (Zm) repetitive / F ctgcttcccggcccgccaac
R ccttatcccgaagttacg / 26 S gene
247 g/c

rDNA 26/18S

/ rDNA 26S – rDNA 18S
X03989 (Zm) repetitive / F GAAAACGGGCACGTGGAAGG
R TACCCCCTCCCAGGACTTCG / 26S-18S intergenic spacer
220 g/c

TC254543

/ Putative Tam3 transposase
AP003311 (Os) repetitive / F CGTGTAAGGTATGCTGCTCG
R GATCGTGGGCCTTCTTAGC / transposase
115 g/c
TC313780
/ Response regulator 4: RR4
AB042261 (Zm) / F GTCAACAAGAGGAAGGCAGC
R CTTCTTTTCCCCTTCCGAACG / 3’-end coding
388 g/c
AZM5_22022 / Response regulator 4: RR4
AB042261 (Zm) / F GTTGTGGAGATTCGGGTGC
R GTAGAGGGAGATGCAGAGG / Putative promoter
194 g

T18745

/ Mitochondrial solute carrier protein homolog
T01729 (At) / F TATCAGACTGAGGATGGTCG
R GGGCTGATGCTGAATGGAG / 3’-end coding
117 g/c
TC261045 / Similar to Allyl alcohol dehydrogenase
AB012241 (At) / F GACCACAAGCACCTCTACC
R CATAGCAACAGTGACACATGG / 5’-end coding
232 g/c
AZM4_134023 / Similar to Allyl alcohol dehydrogenase
AB012241 (At) / F GTATCTGTATCCAAAAGGACC
R CAAATGCAATAAGTGATGGTGA / putative promoter
96 g
TC257813 / Putative protein phosphatase-2C
AY114037 (At) / F TCGACAAGTCAGGAGGTAGC
R TTGGCAGATCCGGCTTCAGG / 5’-end/central coding
407 g – 309 c
TC310872 / Dwarf8
AF413162 (Zm) / F CACAACTCCGGCACGTTCC
R TGACGGGATCGAAGCAACG / 3’-coding and untranslated
694 g/c
dwarf 8 / Dwarf8
AF413162 (Zm) / F atctcatcctccacaggctc
R caatagtctgtcgctgcagg / promoter
494 g
TC271027 / Putative alanine aminotransferase
AP004988 (Os) / F GCGATGTATCTGTTCCCACG
R ATGACAGGATGCCCTCTTGG / 3’-end coding
322 g/c
TC272335 / Expressed protein
AC092557 (Os) / F ACTACCACCGTTTCAGTGC
R ATCTCATGCCTCTCCATCC / all coding
492 g/c
BM073916 / Hypothetical protein
AP002855 (Os) / F GTCGTCCGGAACTGATCAGG
R CCGTGGAGAAGACGCATGG / central coding
280 g/c
AZM4_15378 / Nodulin-like protein
BAC22240 (Os) / F CAGCGGTGTGGGTGCAGGT
R CACCCAGTAAGGCATGGCGA / 5’-end coding
272 g/c
TC248035 / Putative triosephosphate isomerase
AP003241 (Os) / F CTCAGGAGGTTCATGATGG
R GATGAAGACTTGACAGTGGC / 3’-end coding
217 g/c
AI964645 / Similar to thaumatin
L76377 (Os) / F GGTTCGACATCTCCCTCG
R ATCCTATCCGTACGTGTCG / 3’-end coding
381 g/c
TC249385 / Putative arabinogalactan-like protein
AP004194 (Os) / F CGTCGACAAGGTGCTCCTGC
R CTCACAACAGGCAGCCAAGG / 3’-end coding
218 g/c
AZM4_4684 / Putative arabinogalactan-like protein
AP004194 (Os) / F TTATCTGCTCCGTCGCGCAC
R GTTGGTTGATATAGGGGCTCG / putative promoter
176 g
TC251766 / Putative Gamma-thionin
AL662958 (Os) / F CGCGCTCGTCTTCCTGCTG
R ATCCACTCAACTGCGAGACG / all coding - 3’-end untranslated
673 g – 569 c
TC248146
/ Similar to envelope polyprotein (syncytyn)
AJ577596 (Gorilla gorilla) / F ACATAGAGTCCCACGCTGC
R CCGGATGATCCAAATCAAAGG / central coding
157 g/c
TC287704
/ Tryptophan Synthase β 1 (Orp1)
M76684 (Zm) / F AAGGACGTGCACACCGC
R CAGATACAGAACAACAACTC / 3’-end untranslated
207 g/c
AZM4_72470 / Tryptophan Synthase β 1 (Orp1)
M76684 (Zm) / F CATGGACGGACGGCAACC
R CCGGGCTGCCTCGCTTGC / putative promoter
382 g
TC252682 / Similar to Arabidopsis thaliana hypothetical protein
AP002486 (Os) / F GGACTGGGTGCTGGAGACG
R GTCGCGGCGGTAGTTGAGG / 5’-end coding
256 g/c
TC247579 / Glycine-rich protein (Lilium hybrid)
AY072283 / F AGCATCATGGCGTCCAAGG
R ATATACGTAGCAGCGCAGC / all coding
343 g/c
TC285359 / Putative low molecular mass early light-induced protein AP003826 (Os) / F AATGGCAGCGACGGTGATGG
R CGACGAGGCCGAGCATGG / all coding
530 g/c
AZM4_72516
/ Putative low molecular mass early light-induced protein AP003826 (Os) / F CTTGCCTACCCTACCCTG
R TGAGATTCACGGCCGTAGG / putative promoter
201 g
TC289269 / Ethylene-responsive factor-like protein 1 (ERF1)
AY672654 (Zm) / F GCCGCAAGAACCAGTACCG
R GTAGGTGCCGAGCCAGACG / central coding
104 g/c
TC293467
/ Proline-rich protein (PRP)
X60432 (Zm) / F TCATCACCTGCGGCAAGC
R TCTGCATGCAACACTTCGC / 3’-end untranslated
455 g/c
TC261709 / Putative peroxidase
AC090713 (Os) / F ACGCCATCACCAGGCTCG
R GGCCTACCAATGCAAGTGC / 3’-end coding - untranslated
254 g/c
TC306749 / Auxin-independent growth promoter-like protein
AB010076 (At) / F GCCATATATTCTGTCTGATTGCTCC
R TCACTTCCTCATAATAACTTGCACC / central coding
218 g/c
TC292925
/ Putative splicing factor
AP003225 (Os) / F ACAGGATCAGGTGATGAGC
R TGTTTGCCCACTGCATCACG / 3’-end coding
342 g/c
TC263177 / Unknown protein
AC105932 (Os) / F GATCAACCACGGTGCGATGC
R CAGGATGGTTGACACCAGC / 3’-end coding
283 g/c
gapc2 / Glyceraldehyde-3-phosphate dehydrogenase 2
U45858 (Zm) / F AATGGCAAGCTCACTGGC
R CTGTCACCGGTGAAGTCG / 3’-end coding
433 g - 198 c
gapc2
promoter / Glyceraldehyde-3-phosphate dehydrogenase 2
U45858 (Zm) / F tgccttccttccttcttgc
R agcgaaatgcaactcctgg / promoter
231 g
ac1 / Actin 1
J01238 (Zm) / F aaccttcgaatgcccagc
R ctcttggcagtctccagc / 5’-end coding
427 g - 320 c
lg2 / Basic leucine zipper liguleless2
AF036949 (Zm) / F GACAATCTAAGGCACCAGACG
R GTTTTACACCCTCCCTCACC / 3’-end coding
472 g - 261 c
lg2 / Basic leucine zipper liguleless2
AZM5_19442 (Zm) / F TGTACGCAAACCCATCGTTCG
R AACTCTCCTCGCCTTGCACC / 5’end untranslated putative promoter
143 g
id1 / Zinc finger protein ID1
AF058757 (Zm) / F TCTTCTTCCTGCACCAAGAGC
R AGTTGTGGCTCCAGGTCTCG / 3’-end coding
378 g /c
id1 / Zinc finger protein ID1
AZM5_6428 (Zm) / F AGGGAGTGCACTCGATTGCAGC
R GGTCTTCTCTCTTGCAGTTCTGG / 5’end untranslated putative promoter
363 g
gl15 / Ap2-domain regulator Glossy15
U41466 (Zm) / F TTCGTCAGGGGCAGCTCCAGGT
R GACCGTGGACGGATCGCTGC / central coding
673 g - 291 c
gl15
promoter / Ap2-domain regulator Glossy15
AY714877 (Zm) / F GTGTTCTCCATCCTTCCAACC
R TGCACACAAACACAGCACACG / 5’end untranslated - promoter
395 g
an1 / kaurene synthase A L37750 (Zm) / F GCCGTGTGGAAACCGAGTC
R AGCTGGTGGTCCACGATCC / 3’-end coding
328 g - 256 c
an1 / kaurene synthase A AZM5_77937 (Zm) / F AACATAAGCAAGATGGAGAGAGG
R ACGGATACGGATGCGGATACG / 5’end untranslated putative promoter
183 g
TC282552 / GA 3beta-hydroxylas D1 AB056519 (Os) / F CCGGCCGACGACAAGATGC
R TGGGCCAGAGCTTGCGGAG / 5’-end coding
157 g /c
d3 / Dwarf3
U32579 (Zm) / F GTCTTCCTCCACCACTTCC
R AATCTAGCAGCTAGCTACCG / 3’-end coding
247 g - 139 c
d3 / Dwarf3
AZM5_5100 (Zm) / F GGCCACTTACTTGCGTCTGC
R CCTCCCTGTACCACCAGTGC / 5’end untranslated putative promoter
503 g
tb1 / Teosinte branched
U94494 (Zm) / F ATCGGCCAATAACGCACACC
R TGCTGAAAGACGACTCCACC / 3’-end coding
492 g - 397 c
tb1 / Teosinte branched
AZM4_102295 (Zm) / F TTGTGTTGTCGAGAGTGTGATGG
R GGAGGAGAATACAAGGACCTGC / 5’end untranslated putative promoter
431 g
kn1 / Knotted 1
X61308 (Zm) / F CGGCCACTTCATCAACGACG
R TCAGGGATCCATCTGTCAGG / 3’-end coding and untranslated
336 g /c
kn1 / Knotted 1
AZM4_59043 (Zm) / F GAGATGTCCAGGATGTGAGC
R ATGAAGTTCTTGGGGCGAGG / 5’end untranslated putative promoter
480 g
rs1 / Rough Sheath 1
L44133 (Zm) / F TTCTGAAGATGACATGGACCCGAATGGTC
R GAGAACTACAAGCCATGCATAGACGCTAC / 3’-end coding
802 g - 613 c
rs1 / Rough Sheath 1
BZ623681 (Zm) / F ggagcagccatacgtacgtg
R gaaaaggaaccctagcgagc / 5’end untranslated putative promoter
463 g
rs2 / Rough Sheath 2
AF143447 (Zm) / F GAGGTGTGGGAGGAGTTCG
R GGCGTTTACAAGTCGCGTCC / 3’-end coding
341 g /c
rs2 / Rough Sheath 2
AZM4_124222 (Zm) / F TCACATTCCCTCGCCTTGG
R ACGTCAGTGGTGGTTAGCC / 5’end intron
735 g

Supplemental Table 2. List of sequences analyzed and primers.

a: Common sequence name or sequence accession according to indication from TIGR Maize Database.

b: Putative annotation is according to indication from TIGR Maize Database and was generated by searching the representative longest sequence against a non-redundant amino acid (NRAA) database; the annotation and the Genbank accession number for the top NRAA match (P_value of E-10) was used as the putative annotation; Zm: Zea mays; At: Arabidopsis thaliana, Os: Oryza sativa.

c: Forward (F) and reverse (R) primers used for RT-PCR and ChIP analysis are indicated in 5’-3’ orientation.

d: Approximate location and length of the region amplified by the primer combination, using the genomic DNA (g) and cDNA (c) as template.

Different colors indicate different sequences analyzed. Red: repeats. Dark blu: non repetitive sequences that exhibited statistical significant variation of their expression pattern in the 2 AS and/or the 2 OE lines compared to wt. Light blue: non repetitive sequences that did not exhibit significant variation or the statistical significance was observed only in one of the 2 AS or of the 2 OE lines. Black: gapc2 and ac1 genes used as control because showed similar transcript levels in AS, OE, and wt lines. Green: genes related to important aspects of maize development.

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