Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription

Table 1 Number of active genes annotated as bi- or unidirectional

Cell line	Location	Extract	Total	Ensembl		CAGE		Ens+CAGE		Agreement
				Bi	Uni	Bi	Uni	Bi	Uni	(%)
GM12878	Cytosol	PolyA-	3,531	723	2,808	414	3,117	318	2,712	85.8
	Nucleolus	Total	5,244	1143	4,101	926	4,318	641	3,816	85.0
H1hESC	Cell	PolyA-	6,041	1236	4,805	889	5,152	728	4,644	88.9
HepG2	Cytosol	PolyA-	4,315	899	3,416	435	3,880	378	3,359	86.6
	Nucleolus	Total	5,169	1102	4,067	798	4,371	561	3,830	84.9
HUVEC	Cytosol	PolyA-	5,072	1107	3,965	674	4,398	603	3,894	88.7
K562	Cytosol	PolyA-	4,500	893	3,607	423	4,077	363	3,547	86.9
	Nucleolus	Total	2,839	678	2,161	411	2,428	335	2,085	85.2
NHEK	Cytosol	PolyA-	3,521	722	2,799	352	3,169	292	2,739	86.1

The number of active protein-coding genes for each cell line and RNA isolation condition (subcellular location and RNA extract). These genes were annotated as bi- or unidirectional using CAGE, Ensembl, or both methods. The agreement between the CAGE and Ensembl annotations is provided for each dataset.

ISSN: 1471-2164