SUPPLEMENTARY

Chrom. band / Gene / Protein name / E2BSs / RM/TRF
1p36.22 / CFL1 pseudogene 4kb downstream / ACCGcgccCGGT -461bp-ACCGggcgCGGT / +/-
1q32.1 / JARID1B 6kb downstream / histone demethylase JARID1B / ACCGcgccCGGT -294bp- ACCGcgccCGGT / +/+
4q25 / Intergenic region / - / ACCGcaccCGGT -10bp- ACCGctccCGGT / +/+
4q34.1 / HMGB2 / high-mobility group box 2 / ACCGagtcCGGT -126bp-ACCGggccCGGT / -/-
5q31.3 / PCDHA12 / protocadherin alpha 12 / ACCGcggtCGGT -93bp-ACCGgcggCGGT / -/-
6q23.3 / Intergenic region / - / ACCGggcgCGGT -3bp-ACCGggcgCGGT / +/-
7q21.2 / PEX1 / peroxisome biogenesis factor 1 / ACCGggcaCGGT -120bp-ACCGggtgCGGT / +/+
10q24.32 / CNNM2 / cyclin M2 isoform 1 / ACCGcgccCGGT -7bp-ACCGtgccCGGT / +/+
11q14.2 / TMEM135 / transmembrane protein 135 / ACCGtgccCGGT -260bp-ACCGgacaCGGT / +/+
15q26.1 / ZNF774 5kb downstream / zinc finger protein 774 / ACCGggcgCGGT -7bp-ACCAggcgCGGT / +/+
AK127462 3kb downstream / CDNA FLJ45554 fis
17q25.3 / B3GNTL1 / UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1 / 6x ACCGtctgCGGT -26bp- / +/+
17p12 / ARHGAP44 / Rho GTPase activating protein 44. / ACCGctgtCGGT -355bp-ACCGcagtCGGT / -/-
19p13.3 / GNA15 5kb downstream / guanine nucleotide-binding protein alpha-15 subunit / ACCGggcaCGGT -120bp-ACCGgggaCGGT / +/-

Suppl. Table 1. Locations of tandem E2 binding sites in human genome, nearby genes and detection of repeats.

Suppl. Table 2. Locations of single E2BSs with A/T-only spacers in the human genome, nearby genes and detection of repeats.

Position / Gene / Protein name / E2BS / RM
chr1:33117095-33117109 (for) / RBBP4 intron / retinoblastoma binding protein 4 / gACCGatttCGGTc / +
(rev) / ZBTB8OS upstream 1kbp / zinc finger and BTB domain containing 8 opposite
chr1:54195769-54195783 / GLIS1 intron / GLIS family zinc finger 1 / cACCGttttCGGTg / -
chr1:248226607-248226621 / OR2L13 / olfactory receptor, family 2, subfamily L / tACCGttaaCGGTa / -
chr2:7547722-7547736 / closest gene 13kbp / gACCGaattCGGTc / -
chr2:109228768-109228782 / LIMS1_HUMAN intron / LIM and senescent cell antigen-like-containing domain protein 1 / aACCGaaatCGGTg / -
chr3:171503015-171503029 / PLD1 intron / phospholipase D1, phophatidylcholine-specific / tACCGtattCGGTc / -
Q8WYW5 4k downstream
chr4:32181307-32181321 / closest gene 960kbp / gACCGtattCGGTt / +
chr4:37833367-37833381 / PGM2 intron / phosphoglucomutase 2 / tACCGtattCGGTc / +
chr4:101626573-101626587 / closest gene 200kbp / gACCGtataCGGTa / +
chr6:4716998-4717012 / CDYL intron / chromodomain protein, Y chromosome-like isoform / tACCGtataCGGTg / -
chr6:131244897-131244911 / EPB41L2 intron / erythrocyte membrane protein band 4.1-like 2 / aACCGtaaaCGGTg / +
chr7:5919579-5919593 / OCM 800 nt upstream / oncomodulin (Parvalbumin beta) / aACCGaaaaCGGTg / -
chr8:1996660-1996674 / MYOM2 intron / myomesin 2 / aACCGatttCGGTa / -
chr8:123965217-123965231 / ZHX2 exon / zinc fingers and homeoboxes 2 / aACCGatatCGGTg / -
chr8:130760389-130760403 / MLZE downstream 100 bp / melanoma-derived leucine zipper, extra-nuclear / tACCGataaCGGTa / +
chr10:14257623-14257637 / FRMD4A intron / FERM domain containing 4A / aACCGtattCGGTg / -
chr10:62702603-62702617 / RHOBTB1 / Rho-related BTB domain containing 1 / tACCGttatCGGTg / -
chr12:22777121-22777135 / ETNK1 upstream 1kbp / ethanolamine kinase 1 isoform B / tACCGttatCGGTg / -
chr12:76747296-76747310 / OSBPL8 / oxysterol-binding protein-like protein 8 isoform / gACCGtaaaCGGTt / -
chr12:124835737-124835751 / NCOR2 intron / nuclear receptor co-repressor 2 isoform 1 / tACCGttttCGGTa / -
chr13:92849224-92849238 / GPC5 / glypican 5 / tACCGttttCGGTa / -
chr14:81198938-81198952 / C14orf145 / chromosome 14 open reading frame 145 / cACCGatttCGGTt / -
chr14:82049340-82049354 / closest gene 30kbp / gACCGaaatCGGTc / +
chr17:21218143-21218157 / MAP2K3 / mitogen-activated protein kinase kinase 3 / cACCGttatCGGTg / -
chr17:30001937-30001951 / closest gene 120kbp / aACCGatttCGGTc / +
chr17:63156694-63156708 / RGS9 / regulator of G-protein signalling 9 isoform 2 (ekson) / tACCGattaCGGTa / -
chr17:80851103-80851117 / TBCD / beta-tubulin cofactor D / gACCGtttaCGGTg / -
chr18:41151202-41151216 / closest gene 62kbp / aACCGaaaaCGGTa / -
chr18:56880003-56880017 / GRP upstream 8kbp / gastrin-releasing peptide isoform 3 / tACCGatttCGGTg / -
chr19:32207263-32207277 / closest gene 120kbp / aACCGtattCGGTg / -
chr20:49173174-49173188 / PTPN1 / protein tyrosine phosphatase, non-receptor type / tACCGtaatCGGTt / -
chrX:23506463-23506477 / closest gene 92kbp / tACCGatttCGGTg / +
chrX:49116868-49116882 / FOXP3 intron / forkhead box P3 isoform a / tACCGttaaCGGTt / +
chrX:155172554-155172568 / SYBL1 / SYBL1 / aACCGaataCGGTc / -

Suppl. Table 3. PCR primers used in ChIP and mRNA analysis.

Assay / Name / Forward / Reverse
ChIP / URR / CATGGGTGTGTGCAAACCGATT / ACCGGTTTCGGTTCAACCGAT
E1 / GATGCTACAGTGCCCTGTTG / GGCCACCTAGAATCTGTACC
L2 / CTAGGCGTACTGGCATTAGG / GGCTGCATGTGAAGTGGTAG
GAPDH / TACTAGCGGTTTTACGGGCG / ACAGGAGGAGCAGAGAGCGA
ITGB4 / TGCAGAACAGCTCTCAGATG / AAGGGTGGTTGAGTGAATGG
HMGB2 / CTCAGCCCAGCAAGTGGCTC / GTCGGAGGAGGCGGAAACTG
PCDHA / CAGCGCAGGAGGCGCAGTTA / GAGCGTCCGCCTCATCCAGG
ARHGAP44 / AGACGGTGGGCAGGTAGGTC / GGAGCAGCCCTGAACTCGG
RBBP4 / TCGGTTTCTCGGCCTCTGTC / CGCCAAACACTCCGTTACCC
2p25.1 / CTCTTTGGCATTTCCCTCAG / AGAAGGCATGGGTTCCAATC
LIMS1 / TGAAGCAGTAGGAGCAAGTG / GCAACTACGCTGAAACCAAG
OCM / GAGCTGCATCCACTTGATCC / CTGATGTGTCCACCAGTTAC
MYOM2 / TGAGCAGGAAGCGTTTCTTG / AGCTCTGGCGTTCCATATTG
GSDMC / CTCCACCTGGAAACGCAGAG / TCCCTGATGGGCAGTCAGTC
NCOR2 / ACAGCACAGGAGCAGAAACC / GGGAGGCACAGTGACTTTAC
GPC5 / GGTACACTCCCGTTTCTATC / GACTCACTTCCCTCATCTTC
RGS9 / GGTCCATTGAGTCACAATCC / GCAGCATGTTAAGCACTACC
18q12.3 / CACCCATGGTGCCTACATAC / AGCCTTTGGACCTGTGTCTG
PTPN1 / GCCCAAGGCTGATCTTGAAC / AGAATGATGGAGCTCGAGTG
mRNA analysis / HPRT1 / GACTTTGCTTTCCTTGGTCAGG / AGTCTGGCTTATATCCAACACTTCG
E6 / GCAAGCAACAGTTACTGCGACG / GCTTTTCTTCAGGACACAGTGGCT
E7 / GTACGGGATGTAATGGATGG / AACAACGCATGTGCTGTCTC
GAPDH / TTGGTATCGTGGAAGGACTC / TTTCTAGACGGCAGGTCAGG
HMGB / TACGCCTTCTTCGTGCAGAC / CTGTCATAGCGAGCTTTGT
RBBP4 / TCAGTGGTCACCTCACAATG / GGGATTCCAGGAGAAATCAG
ZBTB8OS / CCCAAGGAGATGACTTACAG / CTGAGGGTGCTTGGACAATG
PTPN1 / AGACCCAGGAGGATAAAGAC / CCCGACTTCTAACTTCAGTG

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