Supplementary Table 2 List of primer information and sequences for a group of selected genes of importance to epigenetic modifications and chromatin remodeling and for one housekeeping gene (Actb) used as internal reference. Gene symbols and descriptions have been adopted from the Mouse Genome Informatics database (http://www.informatics.jax.org/). Primer pairs were carefully designed so that they were separated by at least one intron sequence to reduce risk of co-amplified genomic DNA. Additionally, some primers span intron-exon flanks. No primer pair had inter-primer complementarity thus avoiding formation of primer-dimers. All primer sequences were blasted for potential alternative binding sites. Abbreviations: F, forward primer; R, reverse primer; Tm, melting temperature.
a Gene Gene Name (Alias) Primer Sequences 5’-3’ Direction Exon Tm GenBank Product
Symbol Comple- (°C) Accession ID Size (bp)
mentarity
Actb Actin, beta, cytoplasmic F: AAGTGTGACGTTGACATCCG 5 60.00 NM_007393 250
R: GATCCACATCTGCTGGAAGG 6 60.00
Aof2 Amine oxidase (flavin F: GACGTTTGAAGCCACTCTCC 4 59.85 NM_133872 186
containing) domain 2 R: AAGCCAGAAACACCTGAACC 6 59.19
(LSD1)
Dnmt1 DNA methyltransferase 1 F: ACCCCCATCTTCTTGTCTCC 20 60.31 NM_010066 216
R: GGCATTCTCCTTGTCCTCCT 21 60.60 a Gene Gene Name (Alias) Primer Sequences 5’-3’ Direction Exon Tm GenBank Product
Symbol Comple- (°C) Accession ID Size (bp)
mentarity
Dnmt3a DNA methyltransferase 3A F: GAGTCTAACCCCGTGATGATTG 18, 19 60.74 NM_007872 219
R: CTGGTCTTTGCCCTGCTTT 21 60.38
Dnmt3b DNA methyltransferase 3B F: CGACTTGGTGATTGGTGGA 19 60.52 NM_001003961 157
R: CCAGAAGAATGGACGGTTG 20 59.07
Elp3 Elongation protein 3 F: AACAGGGGCCATACTGTGAA 8, 9 60.38 NM_028811 169
homolog R: AACCATCAGGACGAAAAGCA 10 60.64
Gcn5l2 GCN5 general control of F: AAGCCTAACATTGAACAGGGTG 4, 5 60.5 NM_020004 124
amino acid synthesis-like 2 R: TCCAGTAGTTAAGGCAGAGCAG 5 61.2
(yeast)
Hdac1 Histone deacetylase 1 F: AGTCTGTTACTACTACGACGGG 1, 2 60.4 NM_008228 101
R: TGAGCAGCAAATTGTGAGTCAT 2 60.5
Hdac6 Histone deacetylase 6 F: GCTGGTGGCCGTATTATTCTT 23 60.4 NM_010413 117
R: CAAAGTAAGCTGGGGTGGTG 24 60.5
Htatip HIV-1 tat interactive F: TCCCGGTCCAGATCACACTC 5 62.8 NM_178637 130 a Gene Gene Name (Alias) Primer Sequences 5’-3’ Direction Exon Tm GenBank Product
Symbol Comple- (°C) Accession ID Size (bp)
mentarity
protein, homolog (human) R: ACCTTCCGTTTCGTTGAGCG 5, 6 63.0
Mbd1 Methyl-CpG binding F: GAGGACGAGCTACAGCCCTA 10, 11 62.3 NM_013594 131
domain protein 1 R: TTGCCACCCCCGAATTTGG 11 62.9
Mbd2 Methyl-CpG binding F: TGGGAGAAGAGGCTACAAGG 4 59.42 NM_010773 231
domain protein 2, isotype a R: GCAGAGGGGTTGAGATGTGT 5 60.12
and b
Mbd4 Methyl-CpG binding F: TCCCACGGACACAAGTAGAA 4 59.13 NM_010774 235
domain protein 4 R: AGAAACTCCCACAGCACAGG 6 60.30
Myst1 MYST histone F: ACGAGGCGATCACCAAAGTG 4,5 62.5 NM_026370 166
acetyltransferase 1 R: AAGCGGTAGCTCTTCTCGAAC 5 61.8
Myst4 MYST histone F: TGAGGAAAGCATTCCCACATC 16 60.0 NM_017479 178
acetyltransferase monocytic R: ACACTTGTCTGCACTTTAGAGG 17 61.0
leukemia 4
Prmt3 Protein arginine N- F: CAACAGGGTCGTGTTCTCTAC 15, 16 60.0 NM_133740 175 a Gene Gene Name (Alias) Primer Sequences 5’-3’ Direction Exon Tm GenBank Product
Symbol Comple- (°C) Accession ID Size (bp)
mentarity
methyltransferase 3 R: TTCAAAGTCAGGGTCACAATGA 17 60.7
Prmt7 Protein arginine N- F: TACTGCAGGGGCTGACTTCT 4 60.0 NM_145404 131
methyltransferase 7 R: TCACCTCAGTGGAGTGCTTG 5 60.0
Setdb1 SET domain, bifurcated 1 F: CAACTTGCACAATCACGGAAAC 12 60.8 NM_018877 156
R: CAAAGGTGACCGATATGTCTGG 12, 13 60.4
Sirt3 Sirtuin 3 (silent mating type F: ATCCCGGACTTCAGATCCCC 2, 3 62.7 NM_022433 126
information regulation 2, R: CAACATGAAAAAGGGCTTGGG 3 60.0
homolog) 3 (S. cerevisiae)
Sirt4 Sirtuin 4 (silent mating type F: AACCGGACGTCGTTTTCTTT 2 60.1 AK016400 169
information regulation 2 R: ATGGCTATTGGGAGCTTTTG 3 59.2
homolog) 4 (S. cerevisiae)
Sirt5 Sirtuin 5 (silent mating type F: GCGAACGCCAAGCACATAG 3 61.8 NM_178848 149
information regulation 2 R: TGTGATGGGTTTCGAGCAAAG 4 60.8
homolog) 5 (S. cerevisiae) a Gene Gene Name (Alias) Primer Sequences 5’-3’ Direction Exon Tm GenBank Product
Symbol Comple- (°C) Accession ID Size (bp)
mentarity
Sirt7 Sirtuin 7 (silent mating type F: GTCCAGCTTGAAGGTACTAAAG 7, 8 60.3 NM_153056 165
information regulation 2, R: TGAGGAGTTGCATGACATCATC 9 60.1
homolog) 7 (S. cerevisiae)
Smarca2 SWI/SNF related, matrix F: ATGTCGCCAATCTGACCAAC 9 61.0 NM_011416 106
associated, actin dependent R: TCTGCATTCTCTTCAGCCTTC 9, 10 59.7
regulator of chromatin,
subfamily a, member 2
Smarca4 SWI/SNF related, matrix F: CCCACCTAACCTCACCAAGA 28 59.96 NM_011417 232
associated, actin dependent R: CAGCATCACATCCTTCTCCA 30 59.79
regulator of chromatin,
subfamily a, member 4
(BRG1)
Smarca5 SWI/SNF related, matrix F: GGTTTTGCGTCCATTCCTC 9, 10 60.45 NM_053124 173
associated, actin dependent R: TTTTGTCCATCTTCCCTGCT 11 59.67 a Gene Gene Name (Alias) Primer Sequences 5’-3’ Direction Exon Tm GenBank Product
Symbol Comple- (°C) Accession ID Size (bp)
mentarity
regulator of chromatin,
subfamily a, member 5
(SNF2H)
Smyd3 SET and MYND domain F: GCGTTGTTCTCAATGCCGAAT 2 61.8 NM_027188 137
containing 3 R: CCAGAAGTCTCACGGAGTCG 3 61.6
Suv39h1 Suppressor of variegation F: CAGTGTGTGCTGTAAATCTTCT 1 61.0 NM_011514 179
3-9 homolog 1 (Drosophila) R: ATACCCACGCCACTTAACCAG 2 61.8