Activation of anterior HOX genes in hindbrain development during early embryogenesis (Homo sapiens)

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3-5, 9, 16...7, 40, 48, 57, 6116, 8, 40, 42, 616, 1040, 616, 10, 37, 431, 15, 40, 47, 49...6, 10, 3640, 616, 10, 507, 13, 15, 18, 40...7, 12-14, 23...39, 47, 49, 5440, 612537, 43, 45, 677, 40, 48, 51, 5744513834, 52, 627, 21, 56, 57, 6111501, 40, 6540, 611, 6512, 14, 28, 531926, 43cytosolnucleoplasmPOLR2J HIST1H2AB HIST1H2AC H2AFZ HIST1H2BM Me3K5-HIST2H3A HIST1H4 HIST1H2BL HOXB1 mRNAHIST1H2BD HIST1H2AC HIST2H2AA3 PAGR1 PKNOX1 HIST1H2BA H2BFS H2BFS NCOA6 HIST1H2BN Me3K5-H3F3A HIST1H2BH KMT2C HOXA4 geneHIST1H2BO POLR2A Me3K5-HIST2H3A ASH2L HIST1H2AD Me3K5-H3F3A POLR2C POLR2H POLR2E HIST1H2BN POLR2G Me3K-28-H3F3A RBBP7 POLR2J KDM6A NCOA6 HOXC4 geneKMT2C EED HIST2H2AA3 HIST1H2BD HIST1H2AC RBBP7 HIST3H2BB PAXIP1 HIST1H2BH Me3K5-H3F3A RBBP5 POLR2H HIST1H2AD H2AFB1 Me3K5-HIST2H3A HIST1H2BN POLR2A HIST1H2AB HIST2H2AA3 POLR2B H2AFZ Me3K5-HIST1H3A EGR2WDR5 RARA,B:RXRA at HOXB4bivalent chromatinPKNOX1 HIST1H2BJ PAGR1 POLR2J Me3K5-H3F3A HIST1H2BD HIST1H2AD HIST2H2AC HIST1H2BB HIST1H2BL H2BFS WDR5 POLR2L Me3K5-HIST2H3A HIST1H2BM ASH2L HIST1H2BN HIST1H2AJ POLR2D RNA Polymerase IIholoenzyme complex(generic)POLR2B RXRA HIST1H2AD HIST1H2BB HIST1H2BB HOXB3 mRNAZNF335 KMT2C RARA HIST1H2BJ HIST1H2AJ POLR2F KDM6A POLR2C HIST1H2BL NCOA6 HIST1H2BM HIST1H2BJ HIST1H2BB HOXB4 gene PAGR1 POLR2B HIST1H2AB RXRA POLR2C POLR2G H2AFZ SUZ12 H2AFB1 HIST1H4 POLR2I POLR2H POLR2G HIST3H2BB RARA HIST3H2BB PAGR1 H2AFX RBBP7 HIST1H2BA HIST1H2BC HIST2H2AA3 H2AFB1 HIST1H2BO HIST1H2BL HIST1H2BM HIST1H2AC HOXD3 activechromatinPOLR2D POLR2C PBX1 RARA H2AFB1 RBBP7 POLR2B Me3K5-HIST1H3A H2BFS HIST1H4 atRAHIST1H2AJ PBX1:PKNOX1,MEIS1HIST1H2BN HIST2H2AC HOXA3 gene POLR2L KMT2C Me3K5-HIST2H3A HOXA4 gene HIST1H2AB HIST1H2BC HOXA4 mRNAHIST2H2BE HIST1H2BL HIST1H2BO Me3K-28-HIST2H3A HIST1H2BK HIST2H2BE RARB HIST1H2AJ Me3K5-HIST2H3A SUZ12 POLR2K HIST1H2BL Me3K5-H3F3A HIST3H2BB H2AFX H2AFZ RBBP4 ASH2L H2BFS H2AFX HIST1H2BK HIST1H2BA NCOR1 Me3K5-H3F3A RXRA HIST1H2BK HIST1H2AC RXRA HIST1H2BC POLR2A POLR2C HIST1H2BK NCOR1 KMT2D atRA H2AFZ NCOA6 RXRA POLR2G PAGR1 CTCF HIST1H2BC Me3K5-HIST1H3A Me3K5-HIST2H3A RBBP5 EGR2 RBBP7 HIST1H2BK POLR2I POLR2J HIST1H2BB HIST2H2AA3 HIST1H2AB PAXIP1 H2AFX H2AFX HIST1H2AD KDM6A Me3K-28-H3F3A HIST1H2BO HIST1H2BO HIST1H2AB Me3K5-H3F3A H2BFS Me3K5-H3F3A WDR5 H2BFS HOXB2HIST1H2BH H2AFB1 H2AFB1 H2AFZ HOXB3 gene Me3K5-HIST1H3A SUZ12 H2BFS NCOA6 HIST1H2BN KMT2C Me3K5-HIST2H3A HOXA2 gene ASH2L HIST1H2BA HOXB4HOXD4 gene H2BFS ASH2L POLR2E POLR2G HIST1H4 HIST1H2BD HIST1H4 H2AFZ HIST2H2BE RBBP5 H2BFS HIST1H2BN HIST3H2BB HIST1H2BL HIST1H2BO EZH2 ASH2L WDR5 POLR2F HIST1H4 KDM6A HIST1H2BJ HIST1H2BK POLR2C HIST1H2BO PKNOX1 HIST1H2BO KDM6A HIST1H2BD HIST1H2BD HOXA2 mRNAMe3K-28-H3F3A HOXD1 gene Me3K-28-HIST2H3A HIST2H2AA3 H2AFX KMT2D Me3K-28-HIST1H3A POLR2L WDR5 HIST1H2BO Me3K5-HIST1H3A HIST1H2BK AJUBA HIST1H4 NCOA6 HIST1H2BL HIST1H2BL HIST2H2BE EP300 KMT2D HIST2H2AA3 Me3K-28-HIST2H3A HIST1H2AC HIST1H2AD HIST1H2BN H2AFB1 PKNOX1 HIST1H2BM Me3K-28-HIST1H3A atRA:RARA,B:RXRA atactive HOXB4chromatinHIST1H2BK PAGR1 H2AFX POLR2K HIST1H2BK EED H2AFZ HIST1H2BC HIST1H2BN HIST1H2BA PAGR1 HIST1H2AC KMT2C POLR2G RBBP4 HIST1H2BM HIST1H2BN HIST1H2BK Me3K-28-HIST2H3A POLR2A Me3K-28-HIST2H3A HIST1H2BC HIST1H2AD POLR2L HOXB1 HIST2H2AC Me3K-28-HIST2H3A Me3K5-HIST1H3A HIST3H2BB HIST1H2BO HIST1H2BB HOXA1 geneHIST2H2AC EED NCOA6 H2AFX EP300 HIST1H2BJ HIST2H2AA3 HIST1H2BM Me3K5-H3F3A HIST1H2BN Me3K-28-H3F3A Me3K5-H3F3A HOXA2 gene HIST1H2BA HIST1H2BJ EZH2 HIST1H2BC PAXIP1 EZH2 POLR2J POLR2E POLR2J POLR2H H2AFZ HIST1H2BC RARA HIST1H2AJ HIST1H2BD HIST1H2BH Me3K5-HIST2H3A SUZ12 H2AFZ HIST2H2BE HIST1H2AC HIST1H2BM HIST1H2BC POLR2D POLR2B Me3K5-HIST1H3A HIST1H2BA KMT2C POLR2H KMT2D HIST1H2AJ EP300 POLR2D HIST1H2AD POLR2A CNOT6:ZNF335CREBBPNCOA3 HIST1H2AC POLR2J KDM6A RBBP7 ASH2L ASH2L H2BFS HIST2H2BE HIST1H2BJ HIST1H4 HIST1H2BA RARG HIST2H2AC PAGR1 HIST1H2BJ HIST1H2BJ HIST1H2BJ PAXIP1 POLR2L Me3K5-HIST2H3A POLR2I EZH2 HIST3H2BB POLR2B Me3K5-H3F3A HIST1H2BH H2AFX HIST1H2BJ POLR2B H2AFB1 POLR2K Me3K-28-HIST1H3A HIST1H2BD Me3K5-H3F3A PAXIP1 PAXIP1 RARG HIST2H2AA3 H2BFS H2AFZ HOXB3 geneHIST1H2AB HIST1H2BH SUZ12 HIST1H2AD HIST2H2AC POLR2K POLR2F Me3K-28-HIST1H3A Me3K5-H3F3A HIST1H2BM HIST1H2BM H2AFX HOXD4 gene HIST2H2AC MAFBJUN HIST2H2AC Me3K5-HIST1H3A H2AFX H2BFS HIST1H2BD HIST3H2BB EED Me3K-28-HIST2H3A HIST3H2BB POLR2G Me3K5-HIST2H3A CREBBP RXRA HIST2H2AA3 WDR5 HIST2H2AC KDM6A HIST1H2BC HOXB4 geneHIST1H2BM HIST1H2BD HOXB1 HIST1H2BB HIST1H2BC HIST1H2BL HIST1H2BM HIST1H2BJ POLR2C H2AFZ KMT2C HIST1H2BJ atRA HIST1H2BC POLR2C HIST1H2BJ HIST1H2BN HIST1H2AC Me3K5-HIST1H3A HIST1H2AB HIST1H2AB POLR2E HIST2H2AC HIST1H2AC H2AFB1 HIST1H2BH POLR2G HOXB3HOXB2 gene H2BFS HIST1H2BO HIST1H2BN HIST1H2BA POLR2B HOXB3 gene H2BFS HIST2H2AC HIST1H2BB HIST1H4 HOXD4HIST1H2AJ NCOA3 POLR2B NCOA6 HIST2H2AC HIST1H2BM CNOT6 POLR2J HOXD3 gene POLR2D HIST1H2BC HIST1H2BC HIST1H2BD HIST1H2BH HIST1H2BD HIST1H2BA RBBP7 POLR2H HIST2H2BE HIST1H2BB Me3K-28-H3F3A HIST2H2AC HOXD3 mRNAHIST1H2BA HIST1H2BC POLR2E HIST1H2BD MAFB:JUN and EGR2 atactive HOXB3chromatinRQCD1NCOA6 H2AFB1 HIST1H2AC POLR2D POLR2F Me3K-28-HIST2H3A HIST1H2BJ HIST1H2AC H2AFX HIST1H2AJ HIST1H4 HIST1H2AB EP300 HIST1H2BN HIST1H2BC HIST1H2BM HIST3H2BB HIST2H2AC HIST1H2AD HIST2H2AC POLR2F HDAC3HIST1H2AJ RARA,G:RXRA at HOXA1bivalent chromatinPOLR2D H2AFB1 HIST1H2BK RBBP5 HOXB4 gene H2AFZ Me3K5-H3F3A HIST2H2AA3 CTCF EP300HIST1H2BB KMT2D HOXB1 gene H2AFB1 HIST1H2AC Me3K5-HIST1H3A Me3K5-H3F3A RBBP7 HOXB1 H2AFZ POLR2K HIST3H2BB HOXA1 mRNAPOLR2K HIST1H2BK NCOA3 HIST1H2AC HIST3H2BB HIST1H2AJ HIST1H2BH JUNPOLR2D POLR2I KDM6A HIST1H2BB RBBP5 H2AFB1 POLR2G H2AFB1 Me3K5-HIST2H3A HIST2H2BE HIST1H2BB HIST1H2BK POLR2H HIST1H2AC HIST1H2AB POLR2I HIST1H2BO HIST3H2BB HIST1H2BB H2BFS WDR5 PAXIP1 HIST1H2AB H2AFX HIST1H2BA PAXIP1 HIST1H2BK HIST1H2BK HIST1H2BN EZH2 HIST1H2BN H2AFX Me3K5-H3F3A H2AFX PAGR1 HIST1H2AD H2AFB1 POLR2K HIST1H2BL PBX1 atRA HIST1H2BL HIST3H2BB NCOA3 Me3K5-HIST2H3A HOXA2 geneHIST1H2BM ASH2L RXRA H2AFX HIST1H4 RBBP5 HIST1H2BC HOXA2EED HIST1H2BL POLR2J RBBP4 Me3K-28-HIST1H3A EED Me3K5-HIST2H3A EZH2 HIST1H2BB NCOA3HIST1H2BH PAXIP1 HIST1H2AJ HIST1H2BL PAXIP1 ASH2L PBX1 NCOA6 HIST1H4 POLR2F POLR2K HIST1H2BH EZH2 HIST2H2AA3 POLR2L HIST1H2BH HIST1H4 HIST1H2BD HIST1H2BO HIST2H2BE EZH2 Me3K5-HIST1H3A HIST2H2BE HIST1H2AB POLR2G HIST2H2BE PBX1 POLR2I H2AFB1 POLR2L H2BFS HIST1H2AD HIST1H2BO ASH2L KMT2D POLR2A HIST1H2BH Me3K-28-HIST1H3A POLR2I HIST1H2BM Me3K5-H3F3A HIST1H2BK RARA HIST1H2BM HIST1H2BM HIST1H2BB HIST1H2BA HIST3H2BB HIST1H2BA HIST1H2BN EED PBX1 RARA POLR2J POLR2A HIST1H2BH HIST2H2AA3 RARG H2AFB1 POLR2L HIST1H2AC POLR2E HIST1H2AB POLR2C HIST1H2BC HIST1H2AJ EED NCOR1 Me3K5-H3F3A HOXC4 bivalentchromatinHOXB3 activechromatinH2AFB1 H2AFZ EZH2 HIST1H4 H2AFZ POLR2A Me3K5-H3F3A POLR2J RARA HOXA3 bivalentchromatinHIST1H2BM HIST1H2AB PBX1:PKNOX1POLR2L H2AFZ KMT2D H2AFZ HIST1H2BO POLR2L HIST1H2BO HIST1H2BB H2AFB1 NCOR1HIST1H2AJ HIST1H2BO HIST1H2BL HIST2H2BE PAGR1 HIST2H2AA3 Me3K5-HIST1H3A HOXB2 gene RBBP7 H2AFX HOXA3 activechromatinH2AFB1 HIST2H2AC H2BFS POLR2A POLR2E POLR2A PAGR1 HIST1H2BO HIST1H2BN HOXD3Me3K5-HIST1H3A HIST3H2BB HOXA4HOXB2 geneHIST1H2BH HIST1H2BA HIST2H2AA3 Me3K5-HIST2H3A EGR2 HIST1H2BB HIST1H2BM POLR2F Me3K5-H3F3A HIST2H2AA3 ASH2L HIST3H2BB HIST1H2AD HIST3H2BB HIST1H2AD HIST1H2BK HIST1H2AJ HIST1H2AJ HIST1H2BL HIST1H2BH HIST1H2BM EZH2 Me3K5-HIST1H3A H2AFB1 HIST1H2BB POLR2G POLR2E Me3K-28-HIST1H3A H2AFX HIST1H2BH POLR2C Me3K5-H3F3A POLR2H POLR2B HIST1H2BA PAGR1 MEIS1HIST1H2BA PBX1:PKNOX1HIST1H2AC H2BFS HIST2H2AA3 RARB HIST1H2BA POLR2B POLR2D HIST1H2AC HIST1H2AJ HIST1H2BN RARB HOXB1 gene HIST1H2BM HIST1H2BH HIST1H2BN KDM6A KMT2D HIST1H2BC HIST2H2BE NCOA6 H2AFZ Me3K5-HIST2H3A HOXD1 bivalentchromatinHIST1H2BK POLR2H HIST1H2AC KMT2C HIST1H2BH POLR2J HOXB2 gene EED Me3K5-HIST2H3A HIST1H2BO HIST1H2BB EGR2 at active HOXB2chromatinPOLR2F HIST2H2BE HIST1H2BJ HIST2H2AC HIST1H2AC HIST1H2BM SUZ12 EGR2 HIST2H2BE HIST1H2BJ HIST1H2AC H2AFB1 HIST1H2BJ POLR2K PAGR1 HIST1H2AB HIST1H2BK HIST1H2AD HIST1H2BN HIST1H2BH RBBP5 RBBP4 POLR2F HIST1H4 HIST1H2BD HIST1H2BH HIST1H2BH POLR2E Me3K5-HIST2H3A KMT2D H2AFB1 HIST1H2AB HIST1H2AD HIST1H2AD PAGR1 KMT2C HIST1H2BL YY1 HIST1H2BJ HIST1H2BD POLR2B CTCF HOXC4 mRNAPOLR2C HIST1H2BB WDR5 KMT2D H2AFZ HIST1H2BO Me3K5-H3F3A HIST1H2AC MEIS1 HIST2H2BE H2AFB1 HIST1H2BN POLR2D HIST1H2BA HIST1H2BO POLR2K HIST1H4 HIST2H2AC HIST1H2BD HIST1H2BK POLR2E HIST1H2AD HIST1H2BK SUZ12 HIST1H4 HIST3H2BB H2AFZ HIST2H2AC POLR2F HIST2H2AC HIST1H2BL HIST1H2AB H2AFZ PBX1 HIST1H2BD RBBP4 HIST1H4 POLR2F HIST3H2BB RBBP7 HIST1H2AJ KMT2D RARA EP300 HIST1H2AB MAFB POLR2E HOXC4POLR2D HOXA2 gene HIST1H2AB HIST1H2BH POLR2A HIST2H2AA3 HOXA2 gene HIST2H2BE HIST1H2AC POLR2L H2BFS HIST1H2AJ HIST2H2AA3 POLR2G Me3K-28-HIST1H3A HIST3H2BB H2BFS HIST1H2BD HIST1H2BC HIST1H2AJ HIST1H2BD HIST1H2BK HIST1H2BD Me3K-28-H3F3A POLR2H HIST3H2BB HIST1H2BN HIST1H2AJ POLR2D HIST1H2BA H2AFZ POLR2C Me3K5-H3F3A HIST1H2BO HIST1H2BC HIST2H2BE KDM6A SUZ12 Me3K5-HIST2H3A POLR2I RBBP4 ASH2L HIST1H2BA POLR2D HIST1H2BA POLR2E POLR2I Me3K-28-H3F3A HIST1H2BO atRA:RARA,G:RXRA atactive HOXB1chromatinMe3K5-H3F3A H2BFS HIST1H2BO HOXD4 mRNAHIST1H2AB HIST1H2BD POLR2A ASH2L RBBP5 HIST1H2BK HIST2H2AA3 HIST1H2BM POLR2A PAXIP1 POLR2F RBBP4 Me3K-28-H3F3A PCGF2 HIST1H2AB HIST2H2BE HIST1H2BC HIST1H2AD H2AFX atRA RBBP5 HIST1H4 HOXB3 gene HIST1H2BN EED HIST1H2AJ Me3K-28-HIST2H3A EZH2 HIST2H2AA3 KMT2D HIST1H4 POLR2D KMT2C SUZ12 RBBP5 HIST1H2AD NCOA6 H2AFB1 POLR2J PBX1 Me3K5-HIST1H3A HIST2H2AA3 HIST2H2AC HOXB1 geneHIST1H2BN H2AFX HOXB1HIST2H2AC HIST1H2BJ HIST1H2BB H2AFZ POLR2H HIST1H2AJ POLR2H HOXC4 gene Me3K5-HIST1H3A PAXIP1 Me3K-28-H3F3A Me3K5-HIST1H3A HIST1H2BA POLR2A WDR5 HIST1H2BA KMT2D Me3K5-HIST1H3A POLR2I Me3K5-HIST2H3A PCGF2PBX1 HIST1H2BH RBBP7 SUZ12 HOXD1 geneHIST1H2BJ atRA Me3K5-HIST1H3A HIST1H2BO HIST2H2AA3 HOXA3 mRNAMe3K-28-H3F3A HOXA3HIST2H2AC HIST1H2AD HIST1H2AB H2AFZ HOXB3 bivalentchromatinRARA,B:RXRA at HOXA4bivalent chromatinMe3K5-HIST2H3A HIST1H2BM HIST2H2BE HIST1H4 HIST1H2BC EGR2KDM6A POLR2L HIST1H2BC HIST1H2BL HIST1H2AD HIST2H2AA3 RXRA PKNOX1 Me3K5-HIST1H3A HIST1H2BK HIST1H2BJ POLR2H PIAS2POLR2K Me3K5-H3F3A Me3K5-HIST2H3A POLR2G HIST1H2BL NCOA6 H2AFB1 HIST1H2BO POLR2C RARA H2AFX POLR2I HIST3H2BB Me3K5-HIST2H3A Me3K5-HIST2H3A RBBP5 Me3K5-HIST1H3A RARA,B:RXRA at HOXD4bivalent chromatinPOLR2D MEIS1 HOXB1:PBX1:MEIS1,PKNOX1 at active HOXB2 chromatinRBBP4 HIST2H2AA3 HIST1H2BA PKNOX1 HIST1H4 PBX1:PKNOX1HIST1H2AB HIST3H2BB Me3K5-HIST2H3A KMT2C Me3K-28-HIST2H3A HIST1H2AD HIST1H2BN HIST1H2BB HIST1H2AJ HIST2H2BE HIST1H2AB HIST1H2BD POLR2J H2AFB1 EED HOXA3 geneHIST1H2AC HIST1H2BJ HOXB1 HIST1H2BC POLR2K Me3K5-H3F3A HIST2H2BE MLL2,3 complexHIST1H2BA HIST2H2BE H2AFX POLR2H Me3K5-HIST1H3A POLR2E EED Me3K-28-HIST1H3A POLR2F H2AFZ HIST1H2BN Me3K5-HIST2H3A POLR2H HIST1H2BK H2BFS HOXD4 genePOLR2E HOXA2 bivalentchromatinHIST1H2BB ASH2L EZH2 MAFB HIST2H2AA3 HIST1H2BM PAX6HOXD3 geneHIST1H2BL POLR2J POLR2E KMT2D RBBP5 HIST1H2BK HIST1H2AB HIST3H2BB HIST1H2BO HIST2H2BE HIST2H2BE HDAC3 Me3K5-HIST2H3A HIST3H2BB HOXC4 gene HOXA1KMT2D HOXA3 gene HIST2H2AC HIST1H2BA HIST1H2BJ H2BFS HIST1H2AJ HOXD3 gene HIST1H2BD NCOR1 HIST1H2AD POLR2H HOXA3 gene POLR2L RBBP5 Me3K5-H3F3A HIST3H2BB PKNOX1 HIST1H2BB MEIS1 RBBP4 Me3K-28-HIST2H3A POLR2I HIST1H2BM H2AFX HOXB4 mRNAHIST1H2BD Me3K5-HIST2H3A H2AFX H2BFS HIST1H2BJ KMT2C HIST1H2AD HIST1H2BH HIST1H2AC HIST1H4 AJUBAHIST1H2BB HIST1H2BA POLR2G RARB HIST1H2BH POLR2B HIST2H2AA3 HIST1H2BJ HIST1H2AJ HIST2H2AA3 HIST1H2BH POLR2L POLR2J HIST2H2AA3 YY1 Me3K5-HIST1H3A HIST1H2BK H2BFS HIST1H2BH HOXB2 activechromatinPAGR1 HIST1H2AC HIST1H2BH WDR5 ASH2L PAXIP1 KMT2C KDM6A HIST1H2BB Me3K5-HIST1H3A HIST1H2AB HIST1H2BM HIST1H2AB HIST2H2AC H2AFB1 HIST1H4 HIST1H2BB HIST3H2BB EZH2 PAXIP1 HOXD1 gene H2AFX HIST1H2BM POLR2A KMT2C EGR2PAX6 HOXA1 gene Me3K-28-HIST2H3A Me3K5-HIST2H3A POLR2D HIST2H2BE RBBP4 Me3K5-HIST1H3A HIST1H2BO HIST1H2BO HIST1H2BC POLR2A HIST1H2AD Me3K5-HIST1H3A HIST1H4 Me3K5-H3F3A HIST1H2AJ WDR5 Me3K-28-H3F3A HIST1H4 HIST1H2BC HIST1H2BO POLR2E HIST1H2AD HIST1H2BD HOXD3 bivalentchromatinHIST1H2BN HIST1H2AD POLR2L NCOR1 atRA:RARA,B:RXRA atactive HOXA4chromatinMe3K5-HIST1H3A HIST1H2AB POLR2L H2AFZ HIST1H2BJ HIST1H2BK HIST1H4 HIST1H2BB HIST2H2BE HIST1H2BH HIST1H2BL NCOA3 SUZ12 HIST1H2AB HIST1H2BM HIST1H2BL RXRA HIST2H2AA3 KDM6A POLR2I atRA:RARA,B:RXRA atactive HOXD4chromatinHIST1H2BB POLR2I PAXIP1 HIST1H2BL H2AFZ HIST2H2AC Me3K5-H3F3A Me3K5-HIST1H3A H2AFB1 RBBP4 H2AFZ HIST1H4 RBBP7 POLR2G Me3K5-H3F3A RARB HOXB1 gene HIST2H2BE HIST1H2BN HIST1H2AJ HIST1H2BL POLR2F HIST1H4 RXRA HIST1H2BB POLR2F RBBP5 HIST1H2AD HIST1H2AJ atRA:RARA,G:RXRA atactive HOXA1chromatinHIST1H2BL RBBP7 H2AFX HIST1H2BK POLR2K HIST1H2BH HIST1H2AD HIST1H2BK H2BFS HOXD1HOXB1:PBX1:PKNOX1and MEIS1 at activeHOXB1 chromatinHIST1H2BD HOXB2 bivalentchromatinWDR5 PAGR1 HIST1H2BK HIST1H2AC NCOA6 HIST1H2BM HOXB2 mRNAHIST1H2AC EGR2RARB H2BFS H2AFX POLR2B POLR2C POLR2F HOXA1 gene HIST1H2BO HIST2H2BE MAFB,HOXB1:PBX1:PKNOX1at active HOXA3chromatinPRC2 (EZH2) CorePAXIP1 SUZ12 HIST1H2BD HIST1H2AJ H2BFS H2BFS HOXD1 mRNAPOLR2B HIST1H2BJ Me3K-28-HIST1H3A HIST1H2BN HIST2H2AC HIST1H2BN Me3K5-HIST1H3A Me3K5-HIST2H3A HIST1H2AB HIST1H2AJ PKNOX1 HIST1H2BJ WDR5 HIST2H2BE KDM6A HIST1H2AD POLR2K Me3K-28-H3F3A H2BFS Me3K5-HIST1H3A HOXB2 gene HIST1H2BJ Me3K-28-HIST1H3A HIST1H2BC HOXD1 activechromatinHOXA4 gene HIST1H2BJ POLR2I HIST1H2AC H2AFB1 HIST1H2BB HIST1H2BC POLR2G KDM6A H2AFZ HIST1H2BD POLR2K HIST1H2BL WDR5 Me3K-28-HIST1H3A Me3K5-HIST1H3A H2AFZ HIST1H4 HIST2H2AC KDM6A HIST1H2BC RBBP4 HIST2H2AC HIST1H2BD HIST2H2BE KMT2C POLR2B RBBP5 RARG EGR2 at active HOXA2chromatinRBBP4 HIST1H2BL Me3K5-HIST2H3A WDR5 NCOA6 WDR5 HIST2H2AC HIST1H2AC HIST2H2AC POLR2K POLR2I HIST1H2BL HIST1H2BA Me3K5-H3F3A H2AFB1 RBBP5 HIST1H2BA HIST2H2AA3 H2AFX H2AFX HIST1H2BC HIST1H2BD CTCF HIST1H2BL HOXB1:PBX1:PKNOX1 atactive HOXA2chromatinPOLR2C NCOA6 HIST3H2BB HOXC4 activechromatinHIST1H2BA HOXA2 activechromatinEED RARA HIST1H2BL H2AFX HIST3H2BB KMT2D SUZ12 RARA,G:RXRA at HOXB1bivalent chromatinHIST1H4 HIST3H2BB POLR2C HIST1H2AJ H2AFX 488, 40, 611, 15, 40, 47, 49...7, 40, 48, 51486140, 6140, 6140, 611940, 6140, 617, 40, 48, 6140, 6140, 6140, 611, 40, 6511940, 6111, 29, 35, 41, 6627, 56, 6140, 61197, 56, 6118, 40, 611, 40, 651, 15, 40, 47, 49...40, 617, 40, 48, 6140, 61


Description

In mammals, anterior Hox genes may be defined as paralog groups 1 to 4 (Natale et al. 2011), which are involved in development of the hindbrain through sequential expression in the rhombomeres, transient segments of the neural tube that form during development of the hindbrain (reviewed in Alexander et al. 2009, Soshnikova and Duboule 2009, Tumpel et al. 2009, Mallo et al. 2010, Andrey and Duboule 2014). Hox gene activation during mammalian development has been most thoroughly studied in mouse embryos and the results have been extended to human development by in vitro experiments with human embryonal carcinoma cells and human embryonic stem cells.
Expression of a typical anterior Hox gene has an anterior boundary located at the junction between two rhombomeres and continues caudally to regulate segmentation and segmental fate in ectoderm, mesoderm, and endoderm. Anterior boundaries of expression of successive Hox paralog groups are generally separated from each other by 2 rhombomeres. For example, HOXB2 is expressed in rhombomere 3 (r3) and caudally while HOXB3 is expressed in r5 and caudally. Exceptions exist, however, as HOXA1, HOXA2, and HOXB1 do not follow the rule and HOXD1 and HOXC4 are not expressed in rhombomeres. Hox genes within a Hox cluster are expressed colinearly: the gene at the 3' end of the cluster is expressed earliest, and hence most anteriorly, then genes 5' are activated sequentially in the same order as they occur in the cluster.
Activation of expression occurs epigenetically by loss of polycomb repressive complexes and change of bivalent chromatin to active chromatin through, in part, the actions of trithorax family proteins (reviewed in Soshnikova and Duboule 2009). Hox gene expression initiates in the posterior primitive streak that will contribute to extraembryonic mesoderm. Expression then extends anteriorly into the cells that will become the embryo, where expression is first observed in presumptive lateral plate mesoderm and is transmitted to both paraxial mesoderm and neurectoderm formed by gastrulation along the primitive streak (reviewed in Deschamps et al. 1999, Casaca et al. 2014).
Prior to establishment of the rhombomeres, expression of HOXA1 and HOXB1 is initiated near the future site of r3 and caudally by a gradient of retinoic acid (RA). (Mechanisms of retinoic acid signaling are reviewed in Cunningham and Duester 2015.) The RA is generated by the ALDH1A2 (RALDH2) enzyme located in somites flanking the caudal hindbrain and degraded by CYP26 enzymes expressed initially in anterior neural ectoderm of the early gastrula and then throughout most of the hindbrain (reviewed in White and Schilling 2008). HOXA1 with PBX1,2 and MEIS2 directly activate transcription of ALDH1A2 to maintain retinoic acid synthesis in the somitic mesoderm (Vitobello et al. 2011). Differentiation of embryonal carcinoma cells and embryonic stem cells in response to retinoic acid is used to model the process of differentiation in vitro (reviewed in Soprano et al. 2007, Gudas et al. 2013).
HOXA1 appears to set the anterior limit of HOXB1 expression (Barrow et al. 2000). HOXB1 initiates expression of EGR2 (KROX20) in presumptive r3. EGR2 then activates HOXA2 expression in r3 and r5 while HOXB1, together with PBX1 and MEIS:PKNOX1 (MEIS:PREP), activates expression of HOXA2 in r4 and caudal rhombomeres. AP-2 transcription factors maintain expression of HOXA2 in neural crest cells (Maconochie et al. 1999). HOXB1 also activates expression of HOXB2 in r3 and caudal rhombomeres. EGR2 negatively regulates HOXB1 so that by the time rhombomeres appear, HOXB1 is restricted to r4 and HOXA1 is no longer detectable (Barrow et al. 2000). EGR2 and MAFB (Kreisler) then activate HOXA3 and HOXB3 in r5 and caudal rhombomeres. Retinoic acid activates HOXA4, HOXB4, and HOXD4 in r7, the final rhombomere. HOX proteins, in turn, activate expression of genes in combination with other factors, notably members of the TALE family of transcription factors (PBX, PREP, and MEIS, reviewed in Schulte and Frank 2014, Rezsohazy et al. 2015). HOX proteins also participate in non-transcriptional interactions (reviewed in Rezsohazy 2014). In zebrafish, Xenopus, and chicken factors such as Meis3, Fgf3, Fgf8, and vHNF regulate anterior hox genes (reviewed in Schulte and Frank 2014), however less is known about the roles of homologous factors in mammals.
Mutations in HOXA1 in humans have been observed to cause developmental abnormalities located mostly in the head and neck region (Tischfield et al. 2005, Bosley et al. 2008). A missense mutation in HOXA2 causes microtia, hearing impairment, and partially cleft palate (Alasti et al. 2008). A missense mutation in HOXB1 causes a similar phenotype to the Hoxb1 null mutation in mice: bilateral facial palsy, hearing loss, and strabismus (improper alignment of the eyes) (Webb et al. 2012). View original pathway at:Reactome.

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Bibliography

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History

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CompareRevisionActionTimeUserComment
114944view16:46, 25 January 2021ReactomeTeamReactome version 75
113062view10:59, 2 November 2020ReactomeTeamReactome version 74
112296view15:12, 9 October 2020ReactomeTeamReactome version 73
101509view11:37, 1 November 2018ReactomeTeamreactome version 66
101045view21:18, 31 October 2018ReactomeTeamreactome version 65
100576view19:52, 31 October 2018ReactomeTeamreactome version 64
100125view16:37, 31 October 2018ReactomeTeamreactome version 63
99675view15:07, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
99269view12:45, 31 October 2018ReactomeTeamreactome version 62
93879view13:42, 16 August 2017ReactomeTeamreactome version 61
93446view11:23, 9 August 2017ReactomeTeamreactome version 61
87076view14:21, 18 July 2016MkutmonOntology Term : 'regulatory pathway' added !
86538view09:20, 11 July 2016ReactomeTeamNew pathway

External references

DataNodes

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NameTypeDatabase referenceComment
AJUBA ProteinQ96IF1 (Uniprot-TrEMBL)
AJUBAProteinQ96IF1 (Uniprot-TrEMBL)
ASH2L ProteinQ9UBL3 (Uniprot-TrEMBL)
CNOT6 ProteinQ9ULM6 (Uniprot-TrEMBL)
CNOT6:ZNF335ComplexR-HSA-6810135 (Reactome)
CREBBP ProteinQ92793 (Uniprot-TrEMBL)
CREBBPProteinQ92793 (Uniprot-TrEMBL)
CTCF ProteinP49711 (Uniprot-TrEMBL)
EED ProteinO75530 (Uniprot-TrEMBL)
EGR2 ProteinP11161 (Uniprot-TrEMBL)
EGR2 at active HOXA2 chromatinComplexR-HSA-5617477 (Reactome)
EGR2 at active HOXB2 chromatinComplexR-HSA-5617489 (Reactome)
EGR2ProteinP11161 (Uniprot-TrEMBL)
EP300 ProteinQ09472 (Uniprot-TrEMBL)
EP300ProteinQ09472 (Uniprot-TrEMBL)
EZH2 ProteinQ15910 (Uniprot-TrEMBL)
H2AFB1 ProteinP0C5Y9 (Uniprot-TrEMBL)
H2AFX ProteinP16104 (Uniprot-TrEMBL)
H2AFZ ProteinP0C0S5 (Uniprot-TrEMBL)
H2BFS ProteinP57053 (Uniprot-TrEMBL)
HDAC3 ProteinO15379 (Uniprot-TrEMBL)
HDAC3ProteinO15379 (Uniprot-TrEMBL)
HIST1H2AB ProteinP04908 (Uniprot-TrEMBL)
HIST1H2AC ProteinQ93077 (Uniprot-TrEMBL)
HIST1H2AD ProteinP20671 (Uniprot-TrEMBL)
HIST1H2AJ ProteinQ99878 (Uniprot-TrEMBL)
HIST1H2BA ProteinQ96A08 (Uniprot-TrEMBL)
HIST1H2BB ProteinP33778 (Uniprot-TrEMBL)
HIST1H2BC ProteinP62807 (Uniprot-TrEMBL)
HIST1H2BD ProteinP58876 (Uniprot-TrEMBL)
HIST1H2BH ProteinQ93079 (Uniprot-TrEMBL)
HIST1H2BJ ProteinP06899 (Uniprot-TrEMBL)
HIST1H2BK ProteinO60814 (Uniprot-TrEMBL)
HIST1H2BL ProteinQ99880 (Uniprot-TrEMBL)
HIST1H2BM ProteinQ99879 (Uniprot-TrEMBL)
HIST1H2BN ProteinQ99877 (Uniprot-TrEMBL)
HIST1H2BO ProteinP23527 (Uniprot-TrEMBL)
HIST1H4 ProteinP62805 (Uniprot-TrEMBL)
HIST2H2AA3 ProteinQ6FI13 (Uniprot-TrEMBL)
HIST2H2AC ProteinQ16777 (Uniprot-TrEMBL)
HIST2H2BE ProteinQ16778 (Uniprot-TrEMBL)
HIST3H2BB ProteinQ8N257 (Uniprot-TrEMBL)
HOXA1 gene ProteinENSG00000105991 (Ensembl)
HOXA1 geneGeneProductENSG00000105991 (Ensembl)
HOXA1 mRNARnaENST00000343060 (Ensembl)
HOXA1ProteinP49639 (Uniprot-TrEMBL)
HOXA2 active chromatinComplexR-HSA-6810133 (Reactome)
HOXA2 bivalent chromatinComplexR-HSA-5617490 (Reactome)
HOXA2 gene ProteinENSG00000105996 (Ensembl)
HOXA2 geneGeneProductENSG00000105996 (Ensembl)
HOXA2 mRNARnaENST00000222718 (Ensembl)
HOXA2ProteinO43364 (Uniprot-TrEMBL)
HOXA3 active chromatinComplexR-HSA-6810160 (Reactome)
HOXA3 bivalent chromatinComplexR-HSA-5617645 (Reactome)
HOXA3 gene ProteinENSG00000105997 (Ensembl)
HOXA3 geneGeneProductENSG00000105997 (Ensembl)
HOXA3 mRNARnaENST00000317201 (Ensembl)
HOXA3ProteinO43365 (Uniprot-TrEMBL)
HOXA4 gene ProteinENSG00000197576 (Ensembl)
HOXA4 geneGeneProductENSG00000197576 (Ensembl)
HOXA4 mRNARnaENST00000360046 (Ensembl)
HOXA4ProteinQ00056 (Uniprot-TrEMBL)
HOXB1 ProteinP14653 (Uniprot-TrEMBL)
HOXB1 gene ProteinENSG00000120094 (Ensembl)
HOXB1 geneGeneProductENSG00000120094 (Ensembl)
HOXB1 mRNARnaENST00000239174 (Ensembl)
HOXB1:PBX1:MEIS1,PKNOX1 at active HOXB2 chromatinComplexR-HSA-5621009 (Reactome)
HOXB1:PBX1:PKNOX1

and MEIS1 at active

HOXB1 chromatin
ComplexR-HSA-5693638 (Reactome)
HOXB1:PBX1:PKNOX1 at

active HOXA2

chromatin
ComplexR-HSA-5621001 (Reactome)
HOXB1ProteinP14653 (Uniprot-TrEMBL)
HOXB2 active chromatinComplexR-HSA-6810166 (Reactome)
HOXB2 bivalent chromatinComplexR-HSA-5617482 (Reactome)
HOXB2 gene ProteinENSG00000173917 (Ensembl)
HOXB2 geneGeneProductENSG00000173917 (Ensembl)
HOXB2 mRNARnaENST00000330070 (Ensembl)
HOXB2ProteinP14652 (Uniprot-TrEMBL)
HOXB3 active chromatinComplexR-HSA-6810168 (Reactome)
HOXB3 bivalent chromatinComplexR-HSA-5617644 (Reactome)
HOXB3 gene ProteinENSG00000120093 (Ensembl)
HOXB3 geneGeneProductENSG00000120093 (Ensembl)
HOXB3 mRNARnaENST00000311626 (Ensembl)
HOXB3ProteinP14651 (Uniprot-TrEMBL)
HOXB4 gene ProteinENSG00000182742 (Ensembl)
HOXB4 geneGeneProductENSG00000182742 (Ensembl)
HOXB4 mRNARnaENST00000332503 (Ensembl)
HOXB4ProteinP17483 (Uniprot-TrEMBL)
HOXC4 active chromatinComplexR-HSA-5617870 (Reactome)
HOXC4 bivalent chromatinComplexR-HSA-5617885 (Reactome)
HOXC4 gene ProteinENSG00000182742 (Ensembl)
HOXC4 geneGeneProductENSG00000182742 (Ensembl)
HOXC4 mRNARnaENST00000303406 (Ensembl)
HOXC4ProteinP09017 (Uniprot-TrEMBL)
HOXD1 active chromatinComplexR-HSA-5617453 (Reactome)
HOXD1 bivalent chromatinComplexR-HSA-5617473 (Reactome)
HOXD1 gene ProteinENSG00000128645 (Ensembl)
HOXD1 geneGeneProductENSG00000128645 (Ensembl)
HOXD1 mRNARnaENST00000331462 (Ensembl)
HOXD1ProteinQ9GZZ0 (Uniprot-TrEMBL)
HOXD3 active chromatinComplexR-HSA-5617663 (Reactome)
HOXD3 bivalent chromatinComplexR-HSA-5617662 (Reactome)
HOXD3 gene ProteinENSG00000128652 (Ensembl)
HOXD3 geneGeneProductENSG00000128652 (Ensembl)
HOXD3 mRNARnaENST00000249440 (Ensembl)
HOXD3ProteinP31249 (Uniprot-TrEMBL)
HOXD4 gene ProteinENSG00000170166 (Ensembl)
HOXD4 geneGeneProductENSG00000170166 (Ensembl)
HOXD4 mRNARnaENST00000306324 (Ensembl)
HOXD4ProteinP09016 (Uniprot-TrEMBL)
JUN ProteinP05412 (Uniprot-TrEMBL)
JUNProteinP05412 (Uniprot-TrEMBL)
KDM6A ProteinO15550 (Uniprot-TrEMBL)
KMT2C ProteinQ8NEZ4 (Uniprot-TrEMBL)
KMT2D ProteinO14686 (Uniprot-TrEMBL)
MAFB ProteinQ9Y5Q3 (Uniprot-TrEMBL)
MAFB,

HOXB1:PBX1:PKNOX1 at active HOXA3

chromatin
ComplexR-HSA-5617651 (Reactome)
MAFB:JUN and EGR2 at

active HOXB3

chromatin
ComplexR-HSA-5617671 (Reactome)
MAFBProteinQ9Y5Q3 (Uniprot-TrEMBL)
MEIS1 ProteinO00470 (Uniprot-TrEMBL)
MEIS1ProteinO00470 (Uniprot-TrEMBL)
MLL2,3 complexComplexR-HSA-5619379 (Reactome)
Me3K-28-H3F3A ProteinP84243 (Uniprot-TrEMBL)
Me3K-28-HIST1H3A ProteinP68431 (Uniprot-TrEMBL)
Me3K-28-HIST2H3A ProteinQ71DI3 (Uniprot-TrEMBL)
Me3K5-H3F3A ProteinP84243 (Uniprot-TrEMBL)
Me3K5-HIST1H3A ProteinP68431 (Uniprot-TrEMBL)
Me3K5-HIST2H3A ProteinQ71DI3 (Uniprot-TrEMBL)
NCOA3 ProteinQ9Y6Q9 (Uniprot-TrEMBL)
NCOA3ProteinQ9Y6Q9 (Uniprot-TrEMBL)
NCOA6 ProteinQ14686 (Uniprot-TrEMBL)
NCOR1 ProteinO75376 (Uniprot-TrEMBL)
NCOR1ProteinO75376 (Uniprot-TrEMBL)
PAGR1 ProteinQ9BTK6 (Uniprot-TrEMBL)
PAX6 ProteinP26367 (Uniprot-TrEMBL)
PAX6ProteinP26367 (Uniprot-TrEMBL)
PAXIP1 ProteinQ6ZW49 (Uniprot-TrEMBL)
PBX1 ProteinP40424 (Uniprot-TrEMBL)
PBX1:PKNOX1,MEIS1ComplexR-HSA-5693631 (Reactome)
PBX1:PKNOX1ComplexR-HSA-5693627 (Reactome)
PCGF2 ProteinP35227 (Uniprot-TrEMBL)
PCGF2ProteinP35227 (Uniprot-TrEMBL)
PIAS2ProteinO75928 (Uniprot-TrEMBL)
PKNOX1 ProteinP55347 (Uniprot-TrEMBL)
POLR2A ProteinP24928 (Uniprot-TrEMBL)
POLR2B ProteinP30876 (Uniprot-TrEMBL)
POLR2C ProteinP19387 (Uniprot-TrEMBL)
POLR2D ProteinO15514 (Uniprot-TrEMBL)
POLR2E ProteinP19388 (Uniprot-TrEMBL)
POLR2F ProteinP61218 (Uniprot-TrEMBL)
POLR2G ProteinP62487 (Uniprot-TrEMBL)
POLR2H ProteinP52434 (Uniprot-TrEMBL)
POLR2I ProteinP36954 (Uniprot-TrEMBL)
POLR2J ProteinP52435 (Uniprot-TrEMBL)
POLR2K ProteinP53803 (Uniprot-TrEMBL)
POLR2L ProteinP62875 (Uniprot-TrEMBL)
PRC2 (EZH2) CoreComplexR-HSA-212285 (Reactome) The human Polycomb Repressive Complex 2 (PRC2) is homologous to the Drosophila PRC2. The core PRC2 contains EZH2, a histone methyltransferase specific for lysine 27 and lysine 9 of histone H3. The methyltransferase activity of EZH2 is dependent on its association with PRC2. The complex contains other uncharacterized proteins, its composition may vary in different tissues and developmental stages, and the order of assembly of the complex is presently unknown.
RARA ProteinP10276 (Uniprot-TrEMBL)
RARA,B:RXRA at HOXA4 bivalent chromatinComplexR-HSA-5617876 (Reactome)
RARA,B:RXRA at HOXB4 bivalent chromatinComplexR-HSA-5617880 (Reactome)
RARA,B:RXRA at HOXD4 bivalent chromatinComplexR-HSA-5617895 (Reactome)
RARA,G:RXRA at HOXA1 bivalent chromatinComplexR-HSA-5617465 (Reactome)
RARA,G:RXRA at HOXB1 bivalent chromatinComplexR-HSA-5617474 (Reactome)
RARB ProteinP10826 (Uniprot-TrEMBL)
RARG ProteinP13631 (Uniprot-TrEMBL)
RBBP4 ProteinQ09028 (Uniprot-TrEMBL)
RBBP5 ProteinQ15291 (Uniprot-TrEMBL)
RBBP7 ProteinQ16576 (Uniprot-TrEMBL)
RNA Polymerase II

holoenzyme complex

(generic)
ComplexR-HSA-209680 (Reactome)
RQCD1ProteinQ92600 (Uniprot-TrEMBL)
RXRA ProteinP19793 (Uniprot-TrEMBL)
SUZ12 ProteinQ15022 (Uniprot-TrEMBL)
WDR5 ProteinP61964 (Uniprot-TrEMBL)
YY1 ProteinP25490 (Uniprot-TrEMBL)
ZNF335 ProteinQ9H4Z2 (Uniprot-TrEMBL)
atRA MetaboliteCHEBI:15367 (ChEBI)
atRA:RARA,B:RXRA at

active HOXA4

chromatin
ComplexR-HSA-5617873 (Reactome)
atRA:RARA,B:RXRA at

active HOXB4

chromatin
ComplexR-HSA-5617888 (Reactome)
atRA:RARA,B:RXRA at

active HOXD4

chromatin
ComplexR-HSA-5617861 (Reactome)
atRA:RARA,G:RXRA at

active HOXA1

chromatin
ComplexR-HSA-5617448 (Reactome)
atRA:RARA,G:RXRA at

active HOXB1

chromatin
ComplexR-HSA-5617470 (Reactome)
atRAMetaboliteCHEBI:15367 (ChEBI)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
AJUBAArrowR-HSA-5617431 (Reactome)
CNOT6:ZNF335ArrowR-HSA-5617471 (Reactome)
CREBBPR-HSA-5617896 (Reactome)
EGR2 at active HOXA2 chromatinArrowR-HSA-5617483 (Reactome)
EGR2 at active HOXA2 chromatinArrowR-HSA-5617484 (Reactome)
EGR2 at active HOXB2 chromatinArrowR-HSA-5617486 (Reactome)
EGR2 at active HOXB2 chromatinArrowR-HSA-5617492 (Reactome)
EGR2R-HSA-5617484 (Reactome)
EGR2R-HSA-5617492 (Reactome)
EGR2R-HSA-5617661 (Reactome)
EGR2TBarR-HSA-5617454 (Reactome)
EP300R-HSA-5617431 (Reactome)
EP300R-HSA-5617452 (Reactome)
EP300R-HSA-5617859 (Reactome)
EP300R-HSA-5617862 (Reactome)
EP300R-HSA-5617896 (Reactome)
HDAC3ArrowR-HSA-5617431 (Reactome)
HOXA1 geneR-HSA-5617471 (Reactome)
HOXA1 mRNAArrowR-HSA-5617471 (Reactome)
HOXA1 mRNAR-HSA-5617458 (Reactome)
HOXA1ArrowR-HSA-5617452 (Reactome)
HOXA1ArrowR-HSA-5617458 (Reactome)
HOXA2 active chromatinArrowR-HSA-6810139 (Reactome)
HOXA2 active chromatinR-HSA-5617484 (Reactome)
HOXA2 active chromatinR-HSA-5621010 (Reactome)
HOXA2 bivalent chromatinR-HSA-6810139 (Reactome)
HOXA2 geneR-HSA-5617483 (Reactome)
HOXA2 mRNAArrowR-HSA-5617483 (Reactome)
HOXA2 mRNAR-HSA-5617479 (Reactome)
HOXA2ArrowR-HSA-5617479 (Reactome)
HOXA3 active chromatinArrowR-HSA-6810161 (Reactome)
HOXA3 active chromatinR-HSA-5617641 (Reactome)
HOXA3 bivalent chromatinR-HSA-6810161 (Reactome)
HOXA3 geneR-HSA-5617676 (Reactome)
HOXA3 mRNAArrowR-HSA-5617676 (Reactome)
HOXA3 mRNAR-HSA-5617643 (Reactome)
HOXA3ArrowR-HSA-5617643 (Reactome)
HOXA4 geneR-HSA-5617877 (Reactome)
HOXA4 mRNAArrowR-HSA-5617877 (Reactome)
HOXA4 mRNAR-HSA-5617879 (Reactome)
HOXA4ArrowR-HSA-5617879 (Reactome)
HOXB1 geneR-HSA-5617454 (Reactome)
HOXB1 mRNAArrowR-HSA-5617454 (Reactome)
HOXB1 mRNAR-HSA-5617457 (Reactome)
HOXB1:PBX1:MEIS1,PKNOX1 at active HOXB2 chromatinArrowR-HSA-5617486 (Reactome)
HOXB1:PBX1:MEIS1,PKNOX1 at active HOXB2 chromatinArrowR-HSA-5621002 (Reactome)
HOXB1:PBX1:PKNOX1

and MEIS1 at active

HOXB1 chromatin
ArrowR-HSA-5617454 (Reactome)
HOXB1:PBX1:PKNOX1

and MEIS1 at active

HOXB1 chromatin
ArrowR-HSA-5693644 (Reactome)
HOXB1:PBX1:PKNOX1 at

active HOXA2

chromatin
ArrowR-HSA-5617483 (Reactome)
HOXB1:PBX1:PKNOX1 at

active HOXA2

chromatin
ArrowR-HSA-5621010 (Reactome)
HOXB1ArrowR-HSA-5617457 (Reactome)
HOXB1R-HSA-5617641 (Reactome)
HOXB1R-HSA-5621002 (Reactome)
HOXB1R-HSA-5621010 (Reactome)
HOXB1R-HSA-5693644 (Reactome)
HOXB2 active chromatinArrowR-HSA-6810159 (Reactome)
HOXB2 active chromatinR-HSA-5617492 (Reactome)
HOXB2 active chromatinR-HSA-5621002 (Reactome)
HOXB2 bivalent chromatinR-HSA-6810159 (Reactome)
HOXB2 geneR-HSA-5617486 (Reactome)
HOXB2 mRNAArrowR-HSA-5617486 (Reactome)
HOXB2 mRNAR-HSA-5617485 (Reactome)
HOXB2ArrowR-HSA-5617485 (Reactome)
HOXB3 active chromatinArrowR-HSA-6810158 (Reactome)
HOXB3 active chromatinR-HSA-5617661 (Reactome)
HOXB3 bivalent chromatinR-HSA-6810158 (Reactome)
HOXB3 geneR-HSA-5617672 (Reactome)
HOXB3 mRNAArrowR-HSA-5617672 (Reactome)
HOXB3 mRNAR-HSA-5617668 (Reactome)
HOXB3ArrowR-HSA-5617668 (Reactome)
HOXB3TBarR-HSA-5617454 (Reactome)
HOXB4 geneR-HSA-5617867 (Reactome)
HOXB4 mRNAArrowR-HSA-5617867 (Reactome)
HOXB4 mRNAR-HSA-5617881 (Reactome)
HOXB4ArrowR-HSA-5617881 (Reactome)
HOXC4 active chromatinArrowR-HSA-5617866 (Reactome)
HOXC4 active chromatinArrowR-HSA-5617887 (Reactome)
HOXC4 bivalent chromatinR-HSA-5617887 (Reactome)
HOXC4 geneR-HSA-5617866 (Reactome)
HOXC4 mRNAArrowR-HSA-5617866 (Reactome)
HOXC4 mRNAR-HSA-5617855 (Reactome)
HOXC4ArrowR-HSA-5617855 (Reactome)
HOXD1 active chromatinArrowR-HSA-5617445 (Reactome)
HOXD1 active chromatinArrowR-HSA-5617462 (Reactome)
HOXD1 bivalent chromatinR-HSA-5617445 (Reactome)
HOXD1 geneR-HSA-5617462 (Reactome)
HOXD1 mRNAArrowR-HSA-5617462 (Reactome)
HOXD1 mRNAR-HSA-5617446 (Reactome)
HOXD1ArrowR-HSA-5617446 (Reactome)
HOXD3 active chromatinArrowR-HSA-5617642 (Reactome)
HOXD3 active chromatinArrowR-HSA-5617650 (Reactome)
HOXD3 bivalent chromatinR-HSA-5617650 (Reactome)
HOXD3 geneR-HSA-5617642 (Reactome)
HOXD3 mRNAArrowR-HSA-5617642 (Reactome)
HOXD3 mRNAR-HSA-5617652 (Reactome)
HOXD3ArrowR-HSA-5617652 (Reactome)
HOXD4 geneR-HSA-5617874 (Reactome)
HOXD4 mRNAArrowR-HSA-5617874 (Reactome)
HOXD4 mRNAR-HSA-5617864 (Reactome)
HOXD4ArrowR-HSA-5617864 (Reactome)
JUNR-HSA-5617661 (Reactome)
MAFB,

HOXB1:PBX1:PKNOX1 at active HOXA3

chromatin
ArrowR-HSA-5617641 (Reactome)
MAFB,

HOXB1:PBX1:PKNOX1 at active HOXA3

chromatin
ArrowR-HSA-5617676 (Reactome)
MAFB:JUN and EGR2 at

active HOXB3

chromatin
ArrowR-HSA-5617661 (Reactome)
MAFB:JUN and EGR2 at

active HOXB3

chromatin
ArrowR-HSA-5617672 (Reactome)
MAFBR-HSA-5617641 (Reactome)
MAFBR-HSA-5617661 (Reactome)
MEIS1R-HSA-5693644 (Reactome)
MLL2,3 complexR-HSA-5617431 (Reactome)
MLL2,3 complexR-HSA-5617452 (Reactome)
MLL2,3 complexR-HSA-5617492 (Reactome)
MLL2,3 complexR-HSA-5617859 (Reactome)
MLL2,3 complexR-HSA-5617887 (Reactome)
MLL2,3 complexR-HSA-5617896 (Reactome)
MLL2,3 complexR-HSA-6810139 (Reactome)
MLL2,3 complexR-HSA-6810158 (Reactome)
MLL2,3 complexR-HSA-6810159 (Reactome)
MLL2,3 complexR-HSA-6810161 (Reactome)
MLL2,3 complexmim-catalysisR-HSA-5617431 (Reactome)
MLL2,3 complexmim-catalysisR-HSA-5617887 (Reactome)
NCOA3R-HSA-5617431 (Reactome)
NCOA3R-HSA-5617452 (Reactome)
NCOA3R-HSA-5617859 (Reactome)
NCOA3R-HSA-5617862 (Reactome)
NCOA3R-HSA-5617896 (Reactome)
NCOR1ArrowR-HSA-5617431 (Reactome)
NCOR1ArrowR-HSA-5617452 (Reactome)
NCOR1ArrowR-HSA-5617859 (Reactome)
NCOR1ArrowR-HSA-5617862 (Reactome)
NCOR1ArrowR-HSA-5617896 (Reactome)
PAX6R-HSA-5617896 (Reactome)
PBX1:PKNOX1,MEIS1R-HSA-5621002 (Reactome)
PBX1:PKNOX1R-HSA-5617641 (Reactome)
PBX1:PKNOX1R-HSA-5621010 (Reactome)
PBX1:PKNOX1R-HSA-5693644 (Reactome)
PCGF2ArrowR-HSA-5617896 (Reactome)
PIAS2ArrowR-HSA-5617454 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-5617431 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-5617445 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-5617452 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-5617650 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-5617859 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-5617862 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-5617887 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-5617896 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-6810139 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-6810158 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-6810159 (Reactome)
PRC2 (EZH2) CoreArrowR-HSA-6810161 (Reactome)
R-HSA-5617431 (Reactome) As inferred from mouse embryos and cell lines, retinoic acid binds the RARA or RARG receptor in a RAR:RXR dimer bound to the 3' region of HOXA1. Ligand binding by retinoic acid receptors causes dismissal of corepressors such as NCOR1 (Klein et al. 2000), recruitment of coactivators such as NCOA3, and alteration of chromatin at the HOXA1 gene to an active conformation. Similar activation of HOXA1 is also observed in vitro in human breast cancer cells (Chariot et al. 1995). In mouse and Xenopus Hoxa1 acts in a feedback loop to maintain retinoic acid synthesis by directly binding and activating the promoter of the Raldh2 gene.
In addition to recruiting transcription coactivators, retinoic acid also appears to affect histone modifications and DNA methylation. In human embryonal carcinoma cells, KDM6A (UTX) binds the HOXA1 gene upon retinoic acid treatment and demethylates trimethylated lysine-27 of histone H3 (H3K27me3) (Lee et al. 2007). Reduced H3K27me3 is also observed at HOXA1 in lung fibroblasts (Lan et al. 2007). Experiments with mouse embryos lacking Kdm6a and Kdm6b indicate other factors also participate in demethylation of H3K27me3 (Shpargel et al. 2014). Polycomb repressive complex 2 (PRC2), which binds H3K27me3, is also lost during activation by retinoic acid (inferred from mouse cells and also observed in human embryonal carcinoma cells, Lee et al. 2007, Sessa et al. 2007). KDM6A forms complexes with the histone methyltransferases KMT2C,D (MLL2,3) (Lee et al. 2007) which may participate in methylating histone H3 at lysine-4 (H3K4me3), an activating chromatin modification. At the 3' end of the HOXA cluster 5-methylcytosine in CG-rich regions is converted to 5-hydroxymethylcytosine by TET2 during retinoic acid induced differentiation of embryonal carcinoma cells (Bocker et al. 2012). During retinoic acid activation of HOXA genes in human monocytic leukemia cells the HOXA cluster is unfolded and its chromosomal domain is repositioned within the nucleus (Rousseau et al. 2014). Similar large-scale rearrangements may occur during embryogenesis.
In mouse embryos, expression of Hoxa1 occurs in the neural tube, adjacent mesenchyme, paraxial mesoderm, somites, and gut epithelium from rhombomere 4 to the caudal-most region of the embryo. (Rhombomeres are transiently formed segments in the neural tube that will eventually form the hindbrain.)
R-HSA-5617445 (Reactome) As inferred from the Hoxd1 homolog in mouse embryos, HOXD1 is not expressed in hindbrain. In mouse, expression of Hoxd1 begins at E8.5 in caudal lateral mesoderm. At E9.5 to E11.5 Hoxd1 expression is observed in prosomeres p2 and p3 of the diencephalon, dermatomes, urogenital tubercle, and tail bud. Expression is inducible by retinoic acid in neuroblastoma cells, however it is unknown if the induction is direct or indirect (Manohar et al. 1996, Zha et al. 2012). Nerve Growth Factor induces Hoxd1 expression in nociceptors of mouse embryos. As inferred from human posterior HOXD genes in primary human fibroblasts (Lan et al. 2007), other anterior HOX genes, and mouse Hoxd1, the activation of HOXD1 chromatin may be associated with loss of methylation at lysine-27 of histone H3 (H3K27me3) loss of polycomb repressive complex 2 (PRC2), gain of histone acetylation, and gain of methylation at histone H3K4. Like other Hox gene clusters, the HoxD cluster in mouse changes position relative to other loci in the nucleus during activation.
R-HSA-5617446 (Reactome) The HOXD1 mRNA is translated to yield HOXD1 protein.
R-HSA-5617452 (Reactome) As inferred from mouse embryos and cell lines, retinoic acid binds receptors (RARA or RARG) at retinoic acid response elements (RAREs) located 3' to the HOXB1 gene, causing recruitment of coactivators such as NCOA3 and alteration of chromatin at the HOXB1 gene to an active conformation. Similar activation of the HOXB cluster by retinoic acid is observed in human embryonal carcinoma cells (Simeone et al. 1990). In human carcinoma cells and primary fibroblasts, KDM6A (UTX) binds the HOXB1 gene upon retinoic acid treatment (Agger et al. 2007, Lee et al. 2007) and may demethylate trimethylated lysine-27 of histone H3 (H3K27me3). Reduced H3K27me3 is also observed at HOXB1 in lung fibroblasts (Lan et al. 2007). Other demethylases may be redundant with KDM6A. Polycomb repressive complex 2 (PRC2), which binds H3K27me3, is also lost during activation (Lee et al. 2007). KDM6A forms complexes with the histone methyltransferase KMT2C,D (MLL2,3) which may participate in methylating histone H3 at lysine-4 (H3K4me3), an activating chromatin modification (Lee et al. 2007). After activation by retinoic acid HOXB1 maintains its own expression by binding elements in its own promoter and activating expression (Di Rocco et al. 1997).
In mouse embryos, Hoxb1 is expressed in mesoderm and neurectoderm of primitive streak stage embryos and then becomes restricted to rhombomeres of the hindbrain. Before rhombomere formation Hoxb1 is initially expressed in the region that becomes r3-7. After rhombomere formation Hoxb1 becomes restricted to r4 and is also observed in caudal mesoderm. Hoxb1 activates expression of Egr2 (Krox20), a transcription factor that subsequently activates Hoxa2, Hoxb2, and Hoxb3 and represses Hoxb1.
R-HSA-5617454 (Reactome) After activation by retinoic acid, the HOXB1 gene is transcribed to yield mRNA (in embryos in Giampaolo et al. 1989, in human embryonal carcinoma cells in Simeone et al. 1990, Ogura and Evans 1995).
In mouse embryos, Hoxb1 is expressed in mesoderm and neurectoderm of primitive streak stage embryos and then becomes restricted to rhombomeres of the hindbrain. Before rhombomere formation Hoxb1 is initially expressed in the region that becomes r3-7. After rhombomere formation Hoxb1 becomes restricted to r4 and is also observed in caudal mesoderm.
R-HSA-5617457 (Reactome) The HOXB1 mRNA is translated to yield HOXB1 protein. The HOXB1 mRNA is a target of miR-10a (Weiss et al. 2009) and miR-196 (Yekta et al. 2008).
R-HSA-5617458 (Reactome) The HOXA1 mRNA is translated to yield HOXA1 protein (Chen et al. 2013, Chen et al. 2014). MicroRNAs miR-10a (Garzon et al. 2006), let-7c (Zhan et al. 2013), miR-99 (Chen et al. 2013) and miR-100 (Chen et al. 2014) negatively regulate translation in adult cells, however their roles in embryonic cells are unknown.
R-HSA-5617462 (Reactome) The HOXD1 gene is transcribed to yield mRNA (Manohar et al. 1996, Zha et al. 2012). The Hoxd1 homologue in mouse is expressed in caudal lateral mesoderm, prosomeres p2 and p3, dermatomes, urogenital tract, gut endoderm, and tail bud.
R-HSA-5617471 (Reactome) After activation by retinoic acid, the HOXA1 gene is transcribed to yield mRNA (inferred from mouse embryos, also demonstrated in human cancer cells, Chariot et al. 1995, Xu et al. 2014). The mRNA is a target of the microRNAs miR-10a in megakaryocytes (Garzon et al. 2006), miR210 in tumors (Huang et al. 2009), let-7c in non-small cell lung cancer cells (Zhan et al. 2013), miR-99 in epithelial cells (Chen et al. 2013), and miR-100 in tumor cells (Chen et al. 2014), however it is unknown if these play a role in embryogenesis. Opposite strand intergenic transcripts are also observed in adult tissues and placenta (Sessa et al. 2007).
In mouse embryos, expression of Hoxa1 occurs in the neural tube, adjacent mesenchyme, paraxial mesoderm, somites, and gut epithelium from rhombomere 4 to the caudal-most region of the embryo. (Rhombomeres are transiently formed segments in the neural tube that will eventually form the hindbrain.)
R-HSA-5617479 (Reactome) HOXA2 mRNA is translated to yield HOXA2 protein. The microRNA miR-3960 represses translation of HOXA2 (inferred from mouse).
R-HSA-5617483 (Reactome) The HOXA2 is transcribed to yield mRNA (in carcinoma cells, Yates et al. 2010). In mouse embryos Hoxa2 mRNA is observed in rhombomere 2 and caudally through posterior hindbrain, spinal cord, larynx, lungs, vertebrae, sternum, and intestine. Hoxa2 mRNA is a target of microRNA miR-3960 in differentiating mouse osteoblasts.
R-HSA-5617484 (Reactome) As inferred from mouse embryos, HOXA2 expression is directly driven by EGR2 (KROX20) in rhombomeres 3 and 5 (r3, r5) of the hindbrain and by HOXB1 in r4. EGR2 binds sites in the 5' region of the HOXA2 gene. HOXB1 sets up the correct EGR2 expression domain in r3 and thereby indirectly regulates HOXA2 in this region. (HOXA2 is the only HOX gene active in r2. An unknown activator, possibly a transcription factor of the SOX family, may be involved in expression in r2.)
R-HSA-5617485 (Reactome) The HOXB2 mRNA is translated to yield HOXB2 protein (Sengupta et al. 1994, Segara et al. 2005, Zhai et al. 2005).
R-HSA-5617486 (Reactome) The HOXB2 gene is transcribed to yield mRNA (in embryos in Giampaolo et al. 1989, in carcinoma cells in Simeone et al. 1990). In mouse embryos Hoxb2 mRNA is observed in rhombomere 3 and caudally in the neural tube and mesoderm derivatives such as lung.
R-HSA-5617492 (Reactome) As inferrred from mouse embryos, EGR2 (KROX20) binds three sites in the 5' region of the HOXB2 gene and activates expression in rhombomere 3 (r3) and r5. HOXB1 activates HOXB2 in r4 and expression is also observed in r6 and r7.
R-HSA-5617641 (Reactome) As inferred from mouse embryos, the transcription factor MAFB (KREISLER, KMRL) initially activates the HOXA3 gene in rhombomere 5 (r5) and r6. Weaker expression is also observed in r7. HOXA3 autoregulates by binding and activating its own promoter.
R-HSA-5617642 (Reactome) The HOXD3 gene is transcribed to yield mRNA (Zha et al. 2012). In mouse embryos Hoxd3 mRNA is observed in the neural tube with an anterior boundary at the junction of rhombomeres 4-5 and in the dorsal root ganglia, first cervical vertebra, thyroid gland, kidney tubules, esophagus, stomach, and intestines.
R-HSA-5617643 (Reactome) HOXA3 mRNA is translated to yield HOXA3 protein.
R-HSA-5617650 (Reactome) Retinoic acid induces expression of HOXD3 in neuroblastoma cells (Zha et al. 2012) and mouse embryos but it is unknown if the effect is direct or indirect. In mouse embryos the retinoid receptor Rarb is not responsible for the inducibility. As inferred from mouse embryos HOXD3 is expressed in rhombomeres 5, 6, and 7 (r5-7). As inferred from mouse Hoxd3, activation of HOXD3 chromatin is associated with loss of methylation at lysine-27 of histone H3 (H3K27), loss of PRC2, and gain of methylation at H3K4.
R-HSA-5617652 (Reactome) HOXD3 mRNA is translated to yield HOXD3 protein (Zha et al. 2012).
R-HSA-5617661 (Reactome) As inferred from mouse embryos, the MAFB:JUN (KREISLER:JUN) heterodimer binds the rhombomere 5 (r5) enhancer located 5' to the P1 promoter of the HOXB3 gene and activates expression in r5. EGR2 (KROX20) also binds the r5 enhancer is required to activate the HOXB3 gene in r5. After initial activation HOXB3 is hypothesized to maintain its own expression. HOXB3 is expressed most strongly in r5 and more weakly in caudal rhombomeres r6 and r7.
R-HSA-5617668 (Reactome) HOXB3 mRNA is translated to yield HOXB3 protein (Palakurthy et al. 2009, Li et al. 2012, Chen et al. 2013). Translation is repressed by the microRNAs miR-7 and miR-218 (Li et al. 2012) and miR-10A (Weiss et al. 2009).
R-HSA-5617672 (Reactome) The HOXB3 gene is transcribed to yield mRNA (in embryos in Giampaolo et al. 1989, in carcinoma cells in Simeone et al. 1990). The HOXB3 mRNA is a target of the microRNAs miR-7 and miR-218 in breast cancer cells (Li et al. 2012) and miR-10A (Weiss et al. 2009). In mouse embryos Hoxb3 mRNA is observed strongly in rhombomere 5 and more weakly in rhombomeres 6 and 7 of the hindbrain. Hoxb3 mRNA is also observed in mesodermal derivatives including lung, stomach, pancreas, and metanephros, and in neural crest derivatives.
R-HSA-5617676 (Reactome) The HOXA3 gene is transcribed to yield mRNA (Han et al. 2007). In mouse embryos Hoxa3 mRNA is observed in rhombomere 5 and caudally through the central nervous system, ectoderm, and somitic mesoderm. HOXA3 mRNA is a target of the microRNA miR-10a (Han et al. 2007).
R-HSA-5617855 (Reactome) HOXC4 mRNA is translated to yield HOXC4 protein.
R-HSA-5617859 (Reactome) As inferred from mouse embryos, retinoic acid activates the HOXB4 gene in rhombomere 7 (r7) by binding retinoic acid receptor RARB (Folberg et al. 1999) and perhaps RARA in RAR:RXR dimers bound to retinoic acid response elements (RAREs) located in the 3' flanking region of the HOXB4 gene, causing dissociation of corepressors and recruitment of coactivators. HOXB4 maintains its own expression by binding and activating its own promoter.
In human fibroblasts activation of chromatin at the HOXB4 gene accompanied by loss of methylation of lysine-27 at histone H3 (H3K27me3, Lan et al. 2007). Based on observations from mouse embryonic stem cells, Polycomb repressive complex 2 (PRC2), which binds H3K27me3, is anticipated to be lost while methylation of H3K4 is gained, possibly through the action of the histone demethylase KDM6A (UTX) which, in human fibroblasts, binds HOXB4 (Lan et al. 2007). Other factors may be involved in demethylating H3K27me3. KDM6A can form complexes containing the histone methyltransferases KMT2C,D (MLL2,3) which may participate in methylating H3K4 (Lee et al. 2007).
R-HSA-5617862 (Reactome) As inferred from mouse embryos, retinoic acid initially activates expression of the HOXA4 gene in rhombomere 7 (r7) by binding RARB or RARA in dimeric RAR:RXR complexes located at retinoic acid response elements (RAREs) in the 5' flanking region of the HOXA4 promoter (also observed in human teratocarcinoma cells in Doerksen et al. 1996, Sessa et al. 2007), correlating dissociation of corepressors and recruitment of coactivators. In mouse embryos Hoxa4 itself maintains later expression in an autoregulatory loop.
In human fibroblasts (Lan et al. 2007) and teratocarcinoma cells (Sessa et al 2007) activation of HOXA4 chromatin is accompanied by loss of methylation at lysine-27 of histone H3 (H3K27me3) and gain of H3K4me3. The polycomb repressive complex 2 (PRC2), which binds H3K27me3, is also reduced at active HOXA4 chromatin (Lan et al. 2007, Sessa et al. 2007).
R-HSA-5617864 (Reactome) HOXD4 mRNA is translated to yield HOXD4 protein (Zappavigna et al. 1991).
R-HSA-5617866 (Reactome) The HOXC4 gene is transcribed to yield mRNA. In mouse embryos Hoxc4 mRNA is observed caudal to rhombomere 7 in spinal column, prevertebrae, esophagus, metanephric kidney, lung, and trachea.
R-HSA-5617867 (Reactome) The HOXB4 gene is transcribed to yield mRNA (in embryos in Giampaolo et al. 1989, in carcinoma cells in Simeone et al. 1990). The microRNA miR-23a binds the 3' untranslated region of HOXB4 mRNA (Koller et al 2013). In mouse embryos Hoxb4 mRNA is observed in rhombomere 7, paraxial mesoderm of somite 7, and caudally.
R-HSA-5617874 (Reactome) The HOXD4 gene is transcribed to yield mRNA (Moroni et al. 1993, Morrison et al. 1996, Morrison et al. 1997). In mouse embryos Hoxd4 mRNA is observed in rhombomere 7 and caudally in spinal cord and prevertebrae. The HOXD4 promoter region is a target of the microRNA miR-10a, which causes repression of transcription (Tan et al. 2009).
R-HSA-5617877 (Reactome) The HOXA4 gene is transcribed to yield mRNA (Doerksen et al. 1996). In mouse cells, microRNAs miR-196a-2, miR-196b, and miRNA miR-222 target Hoxa4 mRNA untranslated regions. In mouse embryos Hoxa4 mRNA is observed in rhombomere 7, mesoderm (including somites, lung, and kidney), rostral-dorsal stomach, rostral prececal gut, and large intestine.
R-HSA-5617879 (Reactome) The HOXA4 mRNA is translated to yield HOXA4 protein. In mouse cells the microRNAs miR-196a-2, miR-196b, and miR-222 repress expression of Hoxa4.
R-HSA-5617881 (Reactome) HOXB4 mRNA is translated to yield HOXB4 protein. Protein expression is repressed by miR-23a (Koller et al. 2013).
R-HSA-5617887 (Reactome) As inferred from mouse embryos, HOXC4 is expressed at E12.5 caudal to rhombomere 7 (r7) and at the level of prevertebrae 4-5 and caudally. In carcinoma cells treated with retinoic acid (Lee et al. 2007) and primary fibroblasts (Lan et al. 2007) chromatin at HOXC4 loses methylation at lysine-27 of histone H3 (H3K27me3), loses polycomb repressive complex 2 (PRC2), and gains methylation at lysine-4 of histone H3 (H3K4me3). In embryonal carcinoma cells KDM6A (UTX) binds HOXC4 and participates in demethylating H3K27 at HOXC4 (Lee et al. 2007)
R-HSA-5617896 (Reactome) As inferred from mouse embryos, retinoic acid activates the HOXD4 gene in rhombomere 7 (r7) by binding RARB or RARA in RAR:RXR receptor dimers bound to a retinoic acid response element (RAREs) in the 5' flanking region of the gene. Ligand binding by retinoic acid receptors causes dismissal of corepressors such as NCOR1 and recruitment of coactivators such as NCOA3 (Klein et al. 2000). The response of HOXD4 to retinoic acid is also observed in human embryonal carcinoma cells (Moroni et al. 1993, Morrison et al. 1996, Morrison et al. 1997). PAX6 binds near the RARE and is required for maximal activation.
In human fibroblasts chromatin at HOXA genes is activated by loss of methylation at lysine-27 (H3K27me3), loss of Polycomb repressive complex 2 (PRC2), and gain of H3K4me3 (Lan et al. 2007). Similar changes occur at Hoxd4 in mouse embryos. The histone demethylase KDM6A (UTX) binds the HOXD4 gene in human lung fibroblasts and may participate in demethylating H3K27me3 (Lan et al. 2007). Other factors may also be involved in demethylation. KDM6A associates with the histone methyltransferases KMT2C,D (MLL2,3) which may participate in methylating H3K4 (Lee et al. 2007). As inferred from mouse homologs, PCGF2 (MEL18) dissociates from Hoxd4 during activation. After activation by retinoic acid, HOXD4 maintains its own expression by binding and activating its own promoter.
R-HSA-5621002 (Reactome) As inferred from mouse embryos, HOXB1 in a trimeric complex with PBX1 and MEIS1 or PKNOX1 (PREP1) binds an enhancer located 5' to the HOXB2 gene and activates expression of HOXB2 in rhombomere 4 (r4). EGR2 (KROX20) activates HOXB2 in r3 and r5 and expression is also observed in r6 and r7.
R-HSA-5621010 (Reactome) As inferred from mouse homologs, HOXA2 expression is driven by HOXB1 in rhombomere 4 (r4) and EGR2 (KROX20) in r3 and r5. HOXB1 together with PBX and PREP/MEIS cofactors bind an element in the intron of HOXA2. (HOXA2 is the only HOX gene active in r2. An unknown activator, possibly a transcription factor of the SOX family, may be involved in expression in r2.)
R-HSA-5693644 (Reactome) As inferred from mouse embryos and embryonal carcinoma cells, HOXB1 binds with the PBX1:PKNOX1 (PBX1:PREP1) heterodimer (Berthelsen et al. 1998) and MEIS1at the promoter of the HOXB1 gene to maintain expression after initial activation of HOXB1 by retinoic acid signaling. Binding of SOX:OCT heterodimers to the mouse HOXB1 promoter also appear to positively regulate HOXB1 transcription.
R-HSA-6810139 (Reactome) In human cell lines and tissues activation of HOXA2 chromatin by retinoic acid occurs through loss of methylation at lysine-27 of histone H3 (H3K27), dissociation of polycomb repressive complexes, and gain of methylation at H3K4 (Lee et al. 2007 Supplementary, Sakamoto et al. 2007, Sessa et al. 2007). The change in chromatin may be produced by euchromatin spreading from distant 3' retinoic acid response elements. DNA methylation and MBD1 also appear to play a role in maintaining repression at HOXA2 in HeLa cells (Sakamoto et al. 2007). The histone demethylase KDM6A binds HOXA2 (Lee et al. 2007 Supplementary) and may participate in removing H3K27 methylation. KDM6A associates with histone methyltransferases KMT2C,D (MLL2,3) which may participate in methylating H3K4 in embryonal carcinoma cells (Lee et al. 2007, also observed at other HOXA genes in Lan et al. 2007). The conformation of the entire HOXA cluster in the nucleus changes during differentiation of a myeloid leukemia cell line and the conformation changes correlate with gene activity, H3K27me2,3 occurence, and proximity to CTCF binding sites (Rousseau et al. 2014, see also Lonfat and Duboule 2015).
R-HSA-6810158 (Reactome) During activation of HOXB3 by retimoic acid in fibroblasts (Lan et al. 2007) and embryonal carcinoma cells (Lee et al. 2007) chromatin at HOXB3 loses methylation at lysine-27 of histone H3 (H3K27me3), loses PRC2, and gains methylation at H3K4. The demethylase KDM6A (UTX) binds HOXB3 chromatin during activation (Lan et al. 2007, Lee et al. 2007) and may participate in demethylating H3K27me3. KDM6A forms complexes with the histone methyltransferases KMT2C,D (MLL2,3) which may participate in methylating H3K4 (Lee et al. 2007)
R-HSA-6810159 (Reactome) During activation of HOXB1 by retinoic acid in human embryonal carcinoma cells, methylation at lysine-27 of histone H3 (H3K27me3) is lost and methylation at lysine-4 (H3K4me3) is gained (Lan et al. 2007, Lee et al. 2007). The histone demethylase KDM6A (UTX) binds HOXB2 chromatin and may demethylate H3K27me3 (Lee et al. 2007). Other factors may also participate in demethylation. Loss of H3K27me3 is associated with loss of polycomb repressive complex 2 (PRC2) (Lan et al. 2007, Lee et al. 2007). KDM6A forms complexes with the histone methyltransferases KMT2C,D (MLL2,3) which may participate in methylating H3K4 (Lee et al. 2007). The activation of HOXB1 chromatin may be produced by euchromatin spreading from distant 3' retinoic acid response elements.
R-HSA-6810161 (Reactome) In human fibroblasts (Lan et al. 2007) and human embryonic carcinoma cells (Lee et al. 2007, Sessa et al. 2007) treated with retinoic acid HOXA3 chromatin is activated by loss of methylation at lysine-27 of histone H3 (H3K27me3) and gain of H3K4me3. KDM6A (UTX) binds near HOXA3 (Lan et al. 2007, Lee et al. 2007) but does not appear to participate in the loss of H3K27me3. KDM6A forms complexes with the histone methyltransferases KMT2C,D (MLL2,3) which may participate in methylating H3K4 (Lee et al. 2007). Polycomb repressive complex 2 (PRC2), which binds H3K27me3, is also lost during activation of HOXA3 (Lan et al. 2007, Lee et al. 2007, Sessa et al. 2007). The change in chromatin at HOXA3 may result from euchromatin spreading from distant 3' retinoic acid response elements. The chromosomal conformation of the entire HOXA cluster changes during activation (Rousseau et al. 2014).
RARA,B:RXRA at HOXA4 bivalent chromatinR-HSA-5617862 (Reactome)
RARA,B:RXRA at HOXB4 bivalent chromatinR-HSA-5617859 (Reactome)
RARA,B:RXRA at HOXD4 bivalent chromatinR-HSA-5617896 (Reactome)
RARA,G:RXRA at HOXA1 bivalent chromatinR-HSA-5617431 (Reactome)
RARA,G:RXRA at HOXB1 bivalent chromatinR-HSA-5617452 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617431 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617445 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617452 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617484 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617492 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617641 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617650 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617859 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617862 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617887 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5617896 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5621002 (Reactome)
RNA Polymerase II

holoenzyme complex

(generic)
R-HSA-5621010 (Reactome)
RQCD1ArrowR-HSA-5617471 (Reactome)
atRA:RARA,B:RXRA at

active HOXA4

chromatin
ArrowR-HSA-5617862 (Reactome)
atRA:RARA,B:RXRA at

active HOXA4

chromatin
ArrowR-HSA-5617877 (Reactome)
atRA:RARA,B:RXRA at

active HOXB4

chromatin
ArrowR-HSA-5617859 (Reactome)
atRA:RARA,B:RXRA at

active HOXB4

chromatin
ArrowR-HSA-5617867 (Reactome)
atRA:RARA,B:RXRA at

active HOXD4

chromatin
ArrowR-HSA-5617874 (Reactome)
atRA:RARA,B:RXRA at

active HOXD4

chromatin
ArrowR-HSA-5617896 (Reactome)
atRA:RARA,G:RXRA at

active HOXA1

chromatin
ArrowR-HSA-5617431 (Reactome)
atRA:RARA,G:RXRA at

active HOXA1

chromatin
ArrowR-HSA-5617471 (Reactome)
atRA:RARA,G:RXRA at

active HOXB1

chromatin
ArrowR-HSA-5617452 (Reactome)
atRA:RARA,G:RXRA at

active HOXB1

chromatin
ArrowR-HSA-5617454 (Reactome)
atRA:RARA,G:RXRA at

active HOXB1

chromatin
R-HSA-5693644 (Reactome)
atRAArrowR-HSA-5617445 (Reactome)
atRAArrowR-HSA-5617650 (Reactome)
atRAArrowR-HSA-6810139 (Reactome)
atRAArrowR-HSA-6810159 (Reactome)
atRAR-HSA-5617431 (Reactome)
atRAR-HSA-5617452 (Reactome)
atRAR-HSA-5617859 (Reactome)
atRAR-HSA-5617862 (Reactome)
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