Qiang Sun; Guang Chen; Jeffrey W. Streb; Xiaochun Long; Yumei Yang; Christian J. Stoeckert; Joseph M. Miano

Table 2.

Novel SRF target gene summary

Gene	RefSeq no.	CArG Seq	TESS^a	Position^b	GO term	Luciferase^c	SRF binding^d
*Actn1*	NM_134156	CCAAAAATGG	12.78	1500, intron	Cytoskeletal	4.5 ± 0.9^e	EMSA^f
Actr3	NM_023735	CCTTATAAGG	14.49	630, intron	Cytoskeletal	5.8 ± 0.3^e	EMSA^h/ChIP
Aoc3	NM_009675	CCATGTAAGG	11.11	100, 5′UTR	Adhesion	7.1 ± 3.5^g	EMSA^f
Arhe	NM_028810	CCATAAAAGG	13.58	– 100, prom	Cytoskeletal	19.1 ± 1.5^g	EMSA^f
Atp2a2	NM_009722	CCAAATTTGG	12.86	1950, intron	Contractile	3.5 ± 0.5^e	EMSA^f
Casq1	NM_009813	CTTAATATGG	8.06	– 300, prom	Contractile	8.8 ± 1.2^e	EMSA^f
Cfl1	NM_007687	CCTTATTAGG	13.76	– 1400, prom	Cytoskeletal	8.4 ± 0.3ⁱ	EMSA^h/ChIP
*Cfl2*	NM_007688	CCTTATGTGG	9.08	600, intron	Cytoskeletal	5.1 ± 0.7^g	EMSA^h
Coro1a	NM_009898	CCTTAAAAGG	13.68	2160, intron	Cytoskeletal	2.5 ± 0.9^g	EMSA^f
*Dstn*	NM_019771	CCAAAGTAGG	7.39	– 640, prom	Cytoskeletal	8.9 ± 0.4ⁱ	ChIP
Dtna	NM_010087	CTTTATATGG	9.33	1100, intron	Cytoskeletal	8.0 ± 0.6^g	EMSA^f
Efha1	NM_028643	CCTTATTTGG	14.23	– 3320, prom	Contractile	4.3 ± 2.0^e	EMSA^f
*Enah*	NM_010135	CCAAATATGA	7.96	– 2941, prom	Cytoskeletal	2.5 ± 0.8^g	EMSA^f
Enh	NM_019808	CCTTATTTGG	14.23	800, intron	Cytoskeletal	7.4 ± 0.5^g	EMSA^h/ChIP
*Flna*	XM_207130	CCTTATGAGG	8.62	– 2354, prom	Cytoskeletal	6.7 ± 0.4^e	ND
*Flnc*	XM_284175	CCTAAAAAGG	12.42	992, intron	Cytoskeletal	5.6 ± 0.7^e	EMSA^f
Hspb7	NM_013868	CCTTATAAAG	10.32	895, 5′UTR	Cytoskeletal	16.0 ± 1.6^g	EMSA^f
Itga5	NM_010577	ACTTATAAGG	8.85	– 1700, prom	Adhesion	4.7 ± 0.7^e	EMSA^h
Itgb1bp2	NM_013712	CCATGTTTGG	10.85	– 120, prom	Contractile	14.9 ± 3.1ⁱ	EMSA^h
Pfn1	NM_011072	CCAAATAAGG	13.13	1288, intron	Cytoskeletal	6.3 ± 0.7^e	EMSA^h/ChIP
Pln	NM_023129	CCATTTAAGG	13.62	– 1200, prom	Contractile	4.2 ± 0.8^g	EMSA^f
Sdc4	NM_011521	CAATTAAAGG	8.41	2600, intron	Cytoskeletal	2.3 ± 0.1^e	ChIP
Tgfb1i1	NM_009365	CCATACATGG	10.77	– 1300, prom	Adhesion	7.2 ± 0.8^g	EMSA^f
Tln	NM_011602	CCAAATTTGG	12.86	3500, intron	Cytoskeletal	3.7 ± 0.5^e	EMSA^h
Tnnc1	NM_009393	CCATACAAGG	10.30	1150, intron	Contractile	14.6 ± 1.5^g	EMSA^f
Trip6	NM_011639	CCAAAATTGG	12.06	2, 5′UTR	Cytoskeletal	5.7 ± 1.0^e	EMSA^f
Copeb	NM_011803	CCTTATTTGG	14.23	2146, intron	Transcription	11.3 ± 3.3ⁱ	EMSA^f
Elf5	NM_010125	CCATAAAAGG	13.58	3400, intron	Transcription	6.6 ± 2.7^g	EMSA^f
Etv1	NM_007960	CCATTTAAGG	13.62	– 1179, prom	Transcription	2.8 ± 0.5^e	EMSA^f
Fhl1	NM_010211	CCATATATGG	14.86	1900, intron	Transcription	33.8 ± 6.8ⁱ	EMSA^f
Fhl2	NM_010212	CCTTATATGG	14.95	– 140, prom	Transcription	4.2 ± 0.8^e	EMSA^f
Hoxb5	NM_008268	CCATATTTGG	14.13	– 100, prom	Transcription	4.5 ± 0.2^g	EMSA^f
Hoxc6	NM_010465	CCGTTTATGG	6.27	– 1500, prom	Transcription	2.8 ± 0.3^g	UB
Lef1	NM_010703	CCTTAAATGG	14.15	1900, intron	Transcription	6.7 ± 0.6^g	EMSA^f
Nfatc4	NM_023699	CCTTTTTAGG	12.99	300, intron	Transcription	7.1 ± 0.9^g	EMSA^f
Nfyb	NM_010914	CCTTTAAAGG	12.91	950, intron	Transcription	2.9 ± 0.5^g	EMSA^f
Ring1	NM_009066	CCACATAAGG	8.35	– 848, prom	Transcription	3.8 ± 1.0^g	EMSA^f
Tcfap2b	NM_009334	CCATAATTGG	13.32	3200, intron	Transcription	4.7 ± 0.7^e	EMSA^f
Wwtr1	NM_133784	CCAAATATGG	13.59	– 622, prom	Transcription	6.3 ± 0.7^g	EMSA^f
Adm	NM_009627	CCTTATAAGG	14.49	– 730, prom	Signaling	7.5 ± 0.9^e	EMSA^f
Ctgf	NM_010217	CCTTAGAAGG	9.48	1800, nitron	Signaling	5.1 ± 2.9^g	EMSA^f
Dm15	NM_032418	CCTTAAAAGG	13.68	1400, intron	Signaling	4.6 ± 0.7^g	EMSA^h
Dusp6	NM_026268	CCTTGTATGG	11.68	3400, 3′UTR	Signaling	3.2 ± 0.2^g	EMSA^f
Gpc4	NM_008150	CCATTCATGG	10.00	1700, intron	Signaling	2.3 ± 0.5^e	UB
Igf2	NM_010514	CCAAATTTGG	12.86	750, 5′UTR	Signaling	6.1 ± 0.7^g	EMSA^f
Mrgprf	NM_145379	CCAAATAAGG	13.13	– 1500, prom	Signaling	4.1 ± 1.0^g	EMSA^f
P2rx1	NM_008771	GCTTATAAGG	9.38	– 2500, prom	Signaling	10.2 ± 0.7^g	EMSA^f
Rrad	NM_019662	CCTTTTTAGG	12.99	– 1540, prom	Signaling	2.6 ± 0.6^e	EMSA^f
Tspan13	NM_025359	CCAAAAAAGG	12.32	1000, intron	Signaling	2.6 ± 0.4^e	EMSA^f
Bin1	NM_009668	CCATTTTTGG	13.36	3187, intron	Transport	11.7 ± 3.0^e	EMSA^f
Dnajb1	NM_018808	CCTTTTTTGG	13.46	1750, coding	Transport	4.1 ± 1.3^g	EMSA^h
Mrvil	NM_010826	CCTTTTATGG	14.19	– 2681, prom	Transport	5.0 ± 0.7^g	EMSA^f
Car3	NM_007606	CCTAATAAGG	13.22	– 60, prom	Metabolism	5.4 ± 0.9^e	EMSA^f
Mrrf	NM_026422	CCATATTTGG	14.13	2859, intron	Metabolism	11.0 ± 2.1^g	EMSA^f
Urod	NM_009478	CCTAATTAGG	12.50	– 2150, prom	Metabolism	2.2 ± 1.6^e	EMSA^f
Galnt3	NM_015736	CCTAATTAGG	12.50	880, intron	Transferase	5.0 ± 1.5^e	UB
D14Ertd231e	NM_153414	CCATATTAGC	8.57	– 2200, prom	Unknown	4.9 ± 0.2^g	EMSA^f
Impact	NM_008378	CCATTTATGG	14.09	2443, coding	Unknown	6.3 ± 1.3ⁱ	EMSA^h
Lzf	NM_133185	CCTTTTATGG	14.19	– 630, prom	Unknown	4.4 ± 0.9^g	EMSA^f
Shkbp1	NM_138676	CCAAATATGG	13.59	– 1530, prom	Unknown	2.6 ± 0.2^e	EMSA^f

↵a Log-likelihood ratio determined by TESS indicates relative similarity in base composition of novel CArGs to known CArGome (see text)
↵b Position of CArG sequence indicated relative to annotated TSS in mouse genome
↵c Luciferase validations represent fold increases over controls in: ^eRat 2 fibroblasts; ^gC₂C₁₂ myoblasts; or ⁱP19 cells. See Methods for further details
↵d SRF binding was assessed by EMSA for essentially all of the predicted CArG elements and by ChIP for a subset. EMSA validations reflect either the ability of the predicted CArG to compete with SRF binding to a radiolabeled CArG element (^fEMSA) or direct binding of the radiolabeled CArG-containing sequence to in vitro translated SRF (^hEMSA); see Figure 3, B and C, and Methods for further details. (ND) Not determined; (UB) undetectable binding by EMSA or ChIP. Bold italicized genes have conserved CArG sequences ascertained manually as described in Methods

Defining the mammalian CArGome

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