Table 2

Correlation between FAIRE peaks in BC1 and other notable chromatin marks

PeakRegionaSize (bp)“Active”bCTCFcLANAdRTAePromoterDescriptionReference(s)
110083–10467384XXIntragenich
210885–11147262XXORF8/ORF987
311567–12002435XIntragenich
4i17847–18466619XXfXvIL661
522965–23605640XOXXK4.2 OriLyt-L88, 89
6i23758–24220462XXOriLyt-L88, 89
728103–28550447XOXXK6/K7/PAN28, 90
8i29112–29408296XXIntragenic9
951707–52185478XXORF32/ORF29 intronh
1060130–60531401XXORF39/ORF40-41h
1161554–61892338XORF40-41 intronh
1268538–69231693XXXXORF4591
1372133–72463330XORF50 intron92
1474384–74835451XXXXK892
1584695–84973278XXIntragenich
1685687–86245558XXXvIRF193
1791732–92071339XXXvIRF372
18i119144–119418274XXXKaposin/OriLyt-R88, 94, 95
19119546–120371825XOXXOriLyt-R/ALTp7, 88
20121573–121961388XXmiR-K12-5…miR-K12-294, 96
21127436–127830394XXXXXLANApi/K1416, 97, 98
22i127900–128276376XXLANApc12
23i134456–134736280XX5′ ORF75/K15 3′59, 99
24137041–137806765XXgXgXXK15/TR100, 101
  • a KSHV reference genome NC_009333.

  • b Distance to histone mark H3K9/K14-ac/H3K4-me3, ≥250 bp, data set S1; see reference 20.

  • c GEO data set GSM941710 (23); X indicates occupation of CTCF and cohesin; O indicates CTCF without cohesin.

  • d GEO data set GSM941712 (23).

  • e See reference 64.

  • f See reference 61.

  • g 35 TR (nt 137169 to 137969 from NC_009333) added to KSHV reference genome HQ404500.1 in GEO data sets GSM941710/GSM941712.

  • h —, data from the work of Russo et al. (102).

  • i Regions of accessible latent chromatin based on FAIRE.