Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in the HOX clusters

Srivastava, Surabhi; Puri, Deepika; Garapati, Hita Sony; Dhawan, Jyotsna; Mishra, Rakesh K

doi:10.1186/1756-8935-6-8

Epigenetics & Chromatin

Table 1 Potential regulatory elements mapped as HFRs at the murine Hox clusters

From: Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in the HOX clusters

HFR number	Name	Size	Context	HFR number	Name	Size	Context
*HoxA*				*HoxC* continued
1	A_DOWN-1.1	5210	3′ end	8	C_12-11.1	510	Intergenic
2	A_1-2.1	510	NCT	9	C_12-11.2	1460	3′ end
3	A_1-2.2	860	NCT	10	C_12-11.3	1610	NCT
4	A_1-2.3	510	3′ end	11	C_12-11.4	510	Intergenic
5	A_2-3.1	810	Intergenic	12	C_11-10.1	510	NCT
6	A_3-4.1	1410	3′ end	13	C_11-10.2	1510	NCT
7	A_3-4.2	660	Intergenic	14	C_11-10.3	760	NCT
8	A_3-4.3	510	Intergenic	15	C_11-10.4	1260	NCT
9	A_4-5.1	2460	Intergenic	16	C_11-10.5	560	TSS
10	A_4-5.2	2920	Intergenic	17	C_10.1	2230	Genic
11	A_5.1	650	Genic	18	C_9.1	1010	Genic
12	A_6-7.1	610	Intergenic	19	C_9-8.1	760	Intergenic
13	A_6-7.2	510	Intergenic	20	C_9-8.2	850	Intergenic
14	A_7-9.1	510	Intergenic	21	C_8-6.1	710	3′ end
15	A_7-9.2	680	Intergenic	22	C_8-6.2	1370	Intergenic
16	A_7-9.3	1080	Intergenic	23	C_8-6.3	1810	Intergenic
17	A_9-10.1	960	3′ end	24	C_8-6.4	1510	Intergenic
18	A_10-11.1	1060	Intergenic	25	C_6-5.1	600	TSS
19	A_10-11.2	560	NCT	26	C_5-4.1	810	Intergenic
20	A_11.1	560	Genic	27	C_5-4.2	1660	Intergenic
21	A_11-13.1	1110	NCT	28	C_5-4.3	560	Intergenic
22	A_11-13.2	3810	Intergenic	29	C_5-4.4	2660	Intergenic
23	A.UP.1	510	Intergenic	30	C_4-DOWN.1	710	3′ end
24	A.UP.2	660	Intergenic	31	C_DOWN.1	660	Intergenic
25	A.UP.3	560	Intergenic	32	C_DOWN.2	1580	Intergenic
*HoxB*				*HoxD*
1	B_13-9.1	1160	Intergenic	1	D_UP.13	860	Intergenic
2	B_13-9.2	760	Intergenic	2	D_UP.14	1660	Intergenic
3	B_13-9.3	720	Intergenic	3	D_13.1	2030	Genic
4	B_13-9.4	810	Intergenic	4	D_12-11.1	560	3′ end
5	B_9-8.1	800	Intergenic	5	D_11-10.1	1410	Intergenic
6	B_7-6.1	510	NCT	6	D_11-10.2	510	Intergenic
7	B_5-4.1	510	TSS	7	D_10-9.1	910	3′ end
8	B_4-3.1	710	TSS	8	D_9-8.1	2080	3′ end
9	B_3.1	510	Genic	9	D_8-4.1	710	NCT
10	B_3.2	820	Genic	10	D_8-4.2	510	NCT
11	B_2-1.1	560	3′ end	11	D_8-4.3	810	TSS
12	B_2-1.2	760	Intergenic	12	D_8-4.4	760	TSS
13	B_2-1.3	1880	Intergenic	13	D_4-3.1	1510	Intergenic
14	B_2-1.4	690	Intergenic	14	D_4-3.2	1160	TSS
*HoxC*				15	D_3-1.1	760	Intergenic
1	C_UP.26	1020	Intergenic	16	D_3-1.2	510	3′ end
2	C_UP.27	2260	Intergenic	17	D_3-1.3	840	NCT
3	C_UP.28	510	Intergenic	18	D_3-1.4	590	NCT
4	C_UP.29	530	TSS	19	D_3-1.5	2470	NCT
5	C_13.1	1010	Genic	20	D_1-DOWN.1	1360	3′ end
6	C_13.2	1710	Genic	21	D_DOWN.1	3680	Intergenic
7	C_13-12.1	1110	Intergenic	22	D_DOWN.2	1080	Intergenic

93 HFRs at the Hox clusters showing low histone occupancy, as identified from the histone H3 ChIP-on-chip array, are listed along with their contextual location. Nomenclature of the HFR indicates the flanking Hox genes. TSS = HFRs within 1 kb of TSS; 3′end = HFRs at 3′ end of genes; NCT = HFRs within noncoding transcribed regions; Genic = HFRs within Hox genes. Regions located outside the clusters (within 10 kb upstream and downstream) have been associated with the closest Hox gene.

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ISSN: 1756-8935

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