Table 1.

Confirmed Suz12 target genes

No.	Gene name		Position(s) of enrichment
Targets identified by oligonucleotide expression arrays
Genes repressed by SUZ12
1	EIF3S10	Eukaryotic translation initiation factor 3	—500
2	MYT1	Myelin transcription factor	—1700 and +1
3	PSMD11	Proteasome 26S subunit non-ATPase 11	—1000 and +500
4	MGAT4B	Mannosyl glycoprotein acetylglucosaminyltransferase 4B	—3500 and —1000
5	EML4	Echinoderm microtubule-associated-protein-like 4	—500
Genes activated by SUZ12
6	SYBL1	Synaptobrevin-like 1	—2000 and +1
7	SRD6A1	Steroid-5-α-reductase, α polypeptide 1	+1
8	RBMS1	RNA-binding motif single-stranded interacting protein 1	—2000
Targets identified by CpG island arrays
1	DMRTA2	Doublesex-mab-3 (DM) domain-like family A2	—4000 and —2000
2	KCNA1	Potassium voltage-gated channel	—2000
3	LOC119392	Hypothetical protein	+1
4	MFAP1	Microfibrillar-associated protein	+1
5	LOC115811	Similar to RIKEN cDNA 4933433C09	+200
6	CNTFR	Ciliary neurotrophic factor receptor	—2000, —1000, and +1
7	KIAA0254	Sorting nexin 19	—1000
8	TRIM52	Tripartite motif-containing 52	+1
9	RDC1	G-protein-coupled receptor	+1
10	WNT1	Wingless-type MMTV integration site member 1	—2000 and +500
11	KIF2C	Kinesin family member 2C	+1
12	HSPC228	Chromosome 6 open reading frame 55	+1
13	KIS	Kinase interacting with stathmin	+1
14	SLC25A3	Solute carrier family 25 member 3	+300
15	NKX2C	NK2 transcription factor related lcous 3	+600
16	AK056349	Cholinergic receptor, muscarinic 3	—200
17	SRP9	Signal recognition particle 9KDa	+1
18	NUDT2	Nudix-type motif 2	—3000 and +1
19	CNR1*	Cannabinoid receptor 1	+1
20	RBMS1 3′-end	RNA-binding motif single-strand interacting protein	+95000

The position of enrichment indicates the location of Suz12 binding in the promoter relative to the transcriptional start site, which is represented by +1. The top part indicates the genes that were identified by the gene expression analysis (Fig. 3), and the bottom part indicates the genes that were identified by the ChIP-CpG-island arrays (Fig. 6). For the genes identified using the gene expression analyses (Fig. 3), the region spanning from —4 kb to +1 kb relative to the start site was represented on the custom oligonucleotide arrays. Most of the CpG islands detected by the ChIP-CpG analyses (Fig. 6) corresponded to promoter regions. For these cases, —4 kb to +1 kb relative to the start site was analyzed on the custom arrays. However, in some cases the CpG island was located 3′ of a gene (e.g., RBMS1). In these cases, a 5-kb region surrounding the CpG clone was represented on the arrays. The CNR promoter, indicated with an asterisk (^*), was not included in the custom oligonucleotide arrays, but Suz12 binding to that promoter was confirmed by PCR analysis.