Skip to main content

Table 1 Genome-wide hotspots of LXR action

From: Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages

Region number Region coordinates LXR sites Regulated genes Regulated gene names
  Chr Location T09 vehicle Up Down  
R1 1 8412456-11763591 2 1 3 2 RP3-477M7.4, KIF1B, EXOSC10, RERE, ENO1
R3 1 23630263-26071982 2 2 3 1 RPL11, PNRC2, CLIC4, HNRNPR
R4 1 27018838-33511169 2 0 3 3 YTHDF2, SPOCD1, KHDRBS1, SLC9A1, PUM1, SNRNP40
R5 1 43282794-47844512 2 2 6 3 ERMAP, MED8, POMGNT1, KIAA0494, STIL, CMPK1, GPBP1L1, TMEM69, MKNK1
R6 1 150237798-154193105 1 2 8 2 MRPS21, MCL1, ENSA, GABPB2, S100A9, S100A8, RPS27, C1orf43, APH1A, PSMD4
R7 1 154934773-156706753 1 3 4 2 GON4L, KIAA0907, SLC25A44, CCT3, SHC1, C1orf66
R8 1 201798268-207228338 1 2 5 2 IPO9, UBE2T, KDM5B, TMEM183A, RBBP5, ADIPOR1, SOX13
R10 1 226626264-229694443 4 4 4 0 RP11-118H4.1, FTHL2, SPHAR, ABCB10
R14 2 69240275-73460367 0 2 5 2 ANTXR1, GFPT1, SNRNP27, MCEE, C2orf7, TEX261, RAB11FIP5
R20 3 127317065-129041381 1 1 1 2 CNBP, MCM2, C3orf37
R21 3 193585240-196669469 0 2 4 2 TM4SF19, AC092933.3, PAK2, NCBP2, TNK2, AC024937.4
R26 5 137273648-140086267 2 2 6 5 FAM13B, BRD8, ETF1, MATR3, PURA, C5orf53, EGR1, C5orf32, PFDN1, HARS, ZMAT2
R28 5 175818220-179780388 2 1 2 5 RP11-889L3.1, RNF130, PRELID1, HNRNPAB, RUFY1, CANX, GFPT2
R29 5 178977558-180671711 2 0 1 3 RNF130, RUFY1, CANX, GFPT2
R34 6 166778406-170893749 1 2 4 0 BRP44L, CCR6, PSMB1, PDCD2
R39 7 150069060-151361890 1 2 2 2 GIMAP8, FASTK, GIMAP5, AGAP3
R45 8 143354160-145736580 4 5 0 4 TOP1MT, PUF60, BOP1, MFSD3
R48 9 106856540-108403400 4 4 3 0 SMC2, ABCA1, FKTN
R51 9 138541640-140484943 7 9 1 2 EDF1, PMPCA, ZMYND19
R53 11 308106-911658 1 2 1 2 RPLP2, IFITM2, TMEM80
R56 11 63448921-66445276 5 4 2 8 TRMT112, PRDX5, RTN3, GPR137, DPF2, SSSCA1, FIBP, DPP3, RBM4, RBM4B
R57 11 66247879-70053509 1 2 1 4 FADD, DPP3, RBM4, RBM4B, SUV420H1
R59 11 118230301-126138751 1 2 5 6 UBE4A, AP000926.1, TMEM218, EI24, RPUSD4, ATP5L, ARCN1, HINFP, SLC37A2, FAM118B, SRPR
R61 12 56229243-57628892 2 1 5 4 AC034102.1, CNPY2, PTGES3, NACA, PRIM1, MMP19, RAB5B, RNF41,CS
R75 16 108057-2759032 1 4 4 3 STUB1, FAHD1, NDUFB10, PDPK1, RHBDF1, AC141586.5, KCTD5
R76 16 2009518-3072385 3 1 3 2 NDUFB10, PDPK1, TNFRSF12A, AC141586.5, KCTD5
R77 16 28616902-31394319 3 3 2 2 SULT1A1, VKORC1, QPRT, ITGAX
R80 17 3572089-7418491 3 0 5 1 TMEM93, ITGAE, MIS12, TXNDC17, ZBTB4, ACADVL
R83 17 41843489-47502285 2 1 7 4 DUSP3, GJC1, KIAA1267, KPNB1, PNPO, ZNF652, AC004797.1, NMT1, NSF, CDK5RAP3, NFE2L1
R84 17 55015562-59147703 2 2 3 4 COIL, SRSF1, AC005884.1, SUPT4H1, TRIM37, DHX40, TMEM49
R85 17 73512608-76377808 2 1 3 3 C17orf95, SRSF2, BIRC5, TSEN54, RHBDF2, SEC14L1
R86 17 78863340-80685893 5 4 4 5 ARL16, THOC4, SLC16A3, FN3KRP, AC127496.3, ACTG1, HGS, NARF, WDR45L
R93 19 17416476-19617122 3 0 2 2 PDE4C, C19orf50, MRPL34, RFXANK
R95 19 39109721-42789931 3 1 6 2 EIF3K, RPS16, EID2B, PSMC4, HNRNPUL1, RPS19, MRPS12, SERTAD3
R97 19 49298321-51303301 3 0 0 3 BCAT2, BAX, VRK3
R98 19 52359054-56499996 2 1 4 1 ZNF577, ZNF83, LILRB3, NLRP8, RPS9
R101 20 42939823-48809213 2 2 6 3 YWHAB, DNTTIP1, UBE2C, NCOA3, B4GALT5, RNF114, SERINC3, TMEM189-UBE2V1, CEBPB
R107 22 17618400-22901769 1 1 4 7 BID, PI4KA, RANBP1, AC002472.8, CECR5, ATP6V1E1, BCL2L13, COMT, C22orf25, XXbac-B33L19.3, PRAME
R108 22 22890122-25024973 2 0 1 2 MIF, PRAME, GGT1
  1. The genomic regions that contain two or more LXR binding sites and three or more T09-regulated genes (red in Figure 2). The locations of each region, the number of LXR peaks and the number and name of the regulated genes are indicated (for a full summary of all regions and additional statistics see additional file 6: Table S3).