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

Log-likelihood ratio determined by TESS indicates relative similarity in base composition of novel CArGs to known CArGome (see text)

Position of CArG sequence indicated relative to annotated TSS in mouse genome

Luciferase validations represent fold increases over controls in: ^eRat 2 fibroblasts; ^gC₂C₁₂ myoblasts; or ⁱP19 cells. See Methods for further details

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