The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.
More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"P79457-1",
"Q5NCY0-1",
"O70546-1",
"Q3UWM4-1"
],
"evidence": [
{
"id": "R-MMU-4754187",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-4754187"
}
]
},
{
"id": "R-MMU-5617960",
"name": "Retinoic acid activates Hoxb1 chromatin",
"equation": "",
"summary": "In mouse embryos (Marshall et al. 1994, Studer et al. 1994, Wendling et al. 2001, Huang et al. 2002, Roelen et al. 2002), carcinoma cell lines (Ogura and Evans 1995, Chiba et al. 1997, Langston et al. 1997), and embryonic stem cells (Kashyap et al. 2011, Mazzoni et al. 2013) retinoic acid activates Hoxb1 by binding receptors, Rara or Rarg (in embryos in Wendling et al. 2001, in embryonal carcinoma cells in Chiba et al. 1997), at retinoic acid response elements (RAREs) located 3' to the Hoxb1 gene (Marshall et al. 1994, Ogura and Evans 1995, Langston et al. 1997, Huang et al. 2002) and 5' to the Hoxb1 gene (Ogura et al. 1995), causing dismissal of corepressors, recruitment of coactivators, and alteration of chromatin to an active conformation (inferred from Hoxa1, Gillespie and Gudas 2007, Kashyap and Gudas 2010).
In human cells, KDM6A (UTX) binds the HOXB1 gene upon retinoic acid treatment and may demethylate trimethylated lysine-27 of histone H3 (H3K27me3). Demethylation of H3K27me3 at the Hoxb cluster is similarly observed in mouse embryonic stem cells treated with retinoic acid (Kashyap et al. 2011, Mazzoni et al. 2013). Other factors may also cause demethylation of H3K27me3 (Shpargel et al. 2014). Polycomb repressive complex 2 (PRC2), which binds H3K27me3, is also lost during activation (Mazzoni et al. 2013). In human cells KDM6A associates with the methyltransferases KMT2C,D (MLL2,3) which may participate in methylating histone H3 at lysine-4 (H3K4me3), an activating chromatin modification. Gain of H3K4me3 is also observed in mouse embryonic stem cells (Kashyap et al. 2011). The Mll2 complex methylates H3K4 at Hoxb1 in mouse fibroblasts (Wang et al. 2009). In mouse embryos Hoxa1 synergizes with retinoic acid to activate Hoxb1 (Studer et al. 1998, Gavalas et al. 1998). After activation by retinoic acid, Hoxb1 maintains its own expression by forming a ternary Hoxb1:Pknox1:Pbx1 (Hoxb1:Prep1:Pbx1) complex at elements in its own promoter and activating expression (Ogura and Evans 1995, Di Rocco et al. 1997, Ferretti et al. 2005).
Hoxb1 is expressed in mesoderm and neurectoderm of primitive streak stage embryos and then becomes restricted to rhombomeres of the hindbrain (Murphy et al. 1989, Wilkinson et al. 1989, Bogue et al. 1996). Before rhombomere formation Hoxb1 is initially expressed weakly in the region that will become rhombomere 2 (r2) and strongly in the region that becomes r3-7. After rhombomere formation Hoxb1 becomes restricted to r4 and is also observed in caudal mesoderm (Murphy et al. 1989, Arenkiel et al. 2003). Hoxb1 activates expression of Egr2 (Krox20, Wassef et al. 2008), a transcription factor that subsequently activates Hoxa2, Hoxb2, and Hoxb3 but represses Hoxb1.",
"cellular_location": "nucleoplasm",
"input_participant_list": [
"R-ALL-5334804",
"R-MMU-556805",
"R-MMU-556815"
],
"output_participant_list": [
"R-MMU-442459"
],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"O09000-1",
"Q61188-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5617960",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5617960"
}
]
},
{
"id": "R-MMU-5617972",
"name": "Hoxb1 gene is transcribed",
"equation": "",
"summary": "The Hoxb1 gene is transcribed to yield mRNA (Marshall et al. 1994, Studer et al. 1994, Ogura and Evans 1995, Chiba et al. 1997, Di Rocco et al. 1997, Langston et al. 1997, Wendling et al. 2001, Huang et al. 2002, Roelen et al. 2002).
Hoxb1 is expressed in mesoderm and neurectoderm of primitive streak stage embryos and then becomes restricted to rhombomeres of the hindbrain (Murphy et al. 1989, Wilkinson et al. 1989, Bogue et al. 1996). 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 (Murphy et al. 1989, Arenkiel et al. 2003).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5617995"
],
"output_participant_list": [],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"O09000-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5617972",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5617972"
}
]
},
{
"id": "R-MMU-5617990",
"name": "Retinoic acid activates Hoxa1 chromatin",
"equation": "",
"summary": "Experiments in mouse embryos (Frasch et al. 1995, Dupe et al. 1997, Paschaki et al. 2013), embryonal carcinoma cell lines (Langston and Gudas 1992, Langston et al. 1997, Gillespie and Gudas 2007, Kashyap and Gudas 2010), and embryonic stem cells (Lee et al. 2007, Chen and Reese 2011, Kashyap et al. 2011, Mazzoni et al. 2013) indicate retinoic acid binds the Rara or Rarg receptor in a RAR:RXR dimer bound to the 3' region of Hoxa1 and causes activation of Hoxa1 expression. Hoxa1 in turn binds and activates the promoter of the Raldh2 gene to create a feedback loop that maintains retinoic acid synthesis (Vitobella et al. 2011).
Observations in embryonic carcinoma cells indicate the mechanism of activation of retinoic acid receptors proceeds through ligand-dependent release (dismissal) of corepressors such as Ncor1, Ajuba, and Hdac3 followed by recruitment of coactivators such as Ncoa3 and Ep300 (p300) (Horlein et al. 1995, Perissi et al. 2004, Gillespie and Gudas 2007, Hou et al. 2010, Kashyap and Gudas 2010, Bajpe et al. 2013). During activation by retinoic acid chromatin in the region of the Hoxa1 gene is modified from a bivalent state to an active conformation by losing methylation at lysine-27 of histone H3 and associated polycomb repressive proteins (Gillespie and Gudas 2007, Lee et al. 2007, Kashyap and Gudas 2010, Kashyap et al. 2011, Mazzoni et al. 2013). Though experiments with cultured human cells show KDM6A (UTX) and KDM6B (JMJD3) actively demethylate H3K27me3, mouse embryos that lack both Kdm6a and Kdm6b still show loss of H3K27me3 during activation of Hox genes in embryos (Shpargel et al. 2014), therefore other factors may also participate in loss of H3K27me3. A loss of histone deacetylases (HDAC1,2,3) and a gain of histone acetylation (Lee et al. 2007, Urvalek and Gudas 2014) and H3K4me3 (Kashyap et al. 2011) is also associated with activation of Hoxa1 in embryonic stem cells. The Mll2 complex acetylates H3K4 at Hoxa1 in fibroblasts (Wang et al. 2009).
Expression of Hoxa1 occurs in the neural tube, adjacent mesenchyme, paraxial mesoderm, somites, and gut epithelium from the the border between rhombomeres 3 and 4 (r3/r4) to the caudal-most region of the embryo (Baron et al. 1987, Sundin et al, 1990, Murphy and Hill 1991, Godwin et al. 1998, reviewed in Alexander et al. 2009). Prior to formation of rhombomeres, Hoxa1 is expressed weakly in the region of the embryo that will become rhombomere 2 (r2) and strongly in the region that will become r3-7. Expression is transient and ceases by the time rhombomeres form. (Rhombomeres are transiently formed segments in the neural tube that will eventually form the hindbrain.)",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [
"R-MMU-442520",
"R-MMU-5687969"
],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"O88895-1",
"Q8BRH4-1",
"O09000-1",
"Q61188-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5617990",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5617990"
}
]
},
{
"id": "R-MMU-5617999",
"name": "Hoxa1 gene is transcribed",
"equation": "",
"summary": "The Hoxa1 gene is transcribed to yield mRNA in response to retinoic acid in embryos (Frasch et al. 1995, Dupe et al. 1997), teratocarcinoma cells (Langston and Gudas 1992, Langston et al. 1997, Lee et al. 1997, Kashyap and Gudas 2010), and embryonic stem cells (Chen and Reese 2011, reviewed in Gudas and Wagner 2011). Hoxa1 mRNA is observed in the neural tube, adjacent mesenchyme, paraxial mesoderm, somites, and gut epithelium from rhombomere 4 to the caudal-most region of the embryo (Baron et al. 1987, Sundin et al, 1990, Murphy and Hill 1991, Godwin et al. 1998, Makki and Capecchi 2010). (Rhombomeres are transiently formed segments in the neural tube that will eventually form the hindbrain.)
The long non-coding RNA linc-HOXA1 suppresses transcription of Hoxa1 in embryonic stem cells (Maamar et al. 2013).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5617428"
],
"output_participant_list": [
"R-MMU-5617929"
],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"O09000-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5617999",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5617999"
}
]
},
{
"id": "R-MMU-5619411",
"name": "Retinoic acid activates Hoxb4 chromatin",
"equation": "",
"summary": "Retinoic acid activates the Hoxb4 gene in rhombomere 7 (r7) by binding the 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 (Morrison et al. 1997, Gould et al. 1998), causing dissociation of corepressors and recruitment of coactivators (inferred from Hoxa1, Gillespie and Gudas 2007, Kashyap and Gudas 2010). Hoxb4 maintains its own expression by binding and activating its own promoter (Gould et al. 1997, Serpente et al. 2005).
In embryonic stem cells treated with retinoic acid (Kashyap et al. 2011, Mazzoni et al. 2013) and in human cells, activation of chromatin at the Hoxb4 gene is due to loss of methylation of lysine-27 at histone H3 (H3K27me3, Kashyap et al. 2011, Mazzoni et al. 2013), loss of Polycomb repressive complex 2 (PRC2, Mazzoni et al. 2013), and gain of H3K4me3 (Kashyap et al. 2011). The Mll1 and Mll2 complexes methylate H3K4 at Hoxb4 in fibroblasts (Wang et al. 2009). In human cells the histone demethylase KDM6A (UTX) binds the HOXB4 gene and participates in demethylating H3K27me3. Other factors may be involved in demethylation (Shpargel et al. 2014).",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"O09000-1",
"Q61188-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619411",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619411"
}
]
},
{
"id": "R-MMU-5619413",
"name": "Hoxa3 gene is transcribed",
"equation": "",
"summary": "The Hoxa3 gene is transcribed to yield mRNA (Manzanares et al. 1999, Manzanares et al. 2001, Diman et al. 2004, Su and Gudas 2008, Diman et al. 2011). Hoxa3 is expressed in rhombomere 5 and caudally through the central nervous system, ectoderm, and somitic mesoderm (Fainsod et al. 1987, Gaunt 1987).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5619391"
],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619413",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619413"
}
]
},
{
"id": "R-MMU-5619414",
"name": "Hoxa4 gene is transcribed",
"equation": "",
"summary": "The Hoxa4 gene is transcribed to yield mRNA (Behringer et al. 1993, Packer et al. 1998, Packer et al. 2000). MicroRNAs miR-196a-2, miR-196b, and miRNA miR-222 target Hoxa4 mRNA untranslated regions (Arnold et al. 2011). Hoxa4 mRNA is observed in rhombomere 7 (Morrison et al. 1997), mesoderm including somites, lung, and kidney (Behringer et al. 1993, Packer et al 1998, Packer et al. 2000), rostral-dorsal stomach, rostral prececal gut, and large intestine (Pitera et al. 1999).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5619361"
],
"output_participant_list": [],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"O09000-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619414",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619414"
}
]
},
{
"id": "R-MMU-5619417",
"name": "Hoxb4 gene is transcribed",
"equation": "",
"summary": "The Hoxb4 gene is transcribed to yield mRNA (Whiting et al. 1991, Morrison et al. 1997, Gould et al. 1998, Sharpe et al. 1998, Folberg et al. 1999, Pitera et al. 1999, Brend et al. 2003). Hoxb4 mRNA is observed in rhombomere 7, paraxial mesoderm of somite 7, and caudally (Whiting et al. 1991, Brend et al. 2003).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5619373"
],
"output_participant_list": [
"R-MMU-5619409"
],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"O09000-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619417",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619417"
}
]
},
{
"id": "R-MMU-5619418",
"name": "Hoxa2 gene is transcribed",
"equation": "",
"summary": "The Hoxa2 gene is transcribed to yield mRNA (Tan et al. 1992, Maconochie et al. 2001, Tumpel et al. 2007, Lampe et al. 2008, Tumpel et al. 2008). Hoxa2 mRNA is observed in rhombomere 2 and caudally through posterior hindbrain, spinal cord, larynx, lungs, vertebrae, sternum, and intestine (Tan et al. 1992). Hoxa2 mRNA is a target of the microRNA miR-3960 during osteoblast differentiation (Hu et al. 2011).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5619355"
],
"output_participant_list": [
"R-MMU-5619377"
],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08152-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619418",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619418"
}
]
},
{
"id": "R-MMU-5619419",
"name": "Hoxd3 gene is transcribed",
"equation": "",
"summary": "The Hoxd3 gene is transcribed to yield mRNA (Bedford et al. 1995, Tan et al. 1996, Spitz et al. 2001, Chai et al. 2009). Hoxd3 mRNA is observed in the neural tube with an anterior boundary at the junction of rhombomeres 4 and 5 (Bedford et al. 1995) and in the dorsal root ganglia, first cervical vertebra, thyroid gland, kidney tubules, esophagus, stomach, and intestines (Tan et al. 1996).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5619381"
],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619419",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619419"
}
]
},
{
"id": "R-MMU-5619421",
"name": "Hoxd4 gene is transcribed",
"equation": "",
"summary": "The Hoxd4 gene is transcribed to yield mRNA (Featherstone et al. 1988, Popperl and Featherstone 1993, Folberg et al. 1997, Zhang et al. 1997, Folberg et al. 1999, Pitera et al. 1999, Zhang et al. 2000, Wendling et al. 2001, Nolte et al. 2003, Serpente et al. 2005, Kobrossy et al. 2006, Nolte et al. 2006). Hoxd4 mRNA is observed in rhombomere 7 and caudally in spinal cord and prevertebrae of embryos (Featherstone et al. 1988).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5619403"
],
"output_participant_list": [],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"O09000-1",
"P45481-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619421",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619421"
}
]
},
{
"id": "R-MMU-5619424",
"name": "Mafb and Hoxb1:Pbx1:Pknox1 (Hoxb1:Pbx1:Prep1) activate Hoxa3 expression",
"equation": "",
"summary": "The transcription factor Mafb (Kreisler, Kmrl) initially activates the Hoxa3 gene in rhombomere 5 (r5) and r6 (Manzanares et al. 1999). Weaker expression is also observed in r7. Hoxa3 autoregulates by binding and activating its own promoter (Manzanares et al. 2001).",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"Q61188-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619424",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619424"
}
]
},
{
"id": "R-MMU-5619425",
"name": "Hoxc4 gene is transcribed",
"equation": "",
"summary": "The Hoxc4 gene is transcribed to yield mRNA (Geada et al. 1992, Pitera et al. 1999, Liu and Zhu 2000). In embryos Hoxc4 mRNA is observed caudal to rhombomere 7 in spinal column, prevertebrae, esophagus, metanephric kidney, lung, and trachea (Geada et al. 1992).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5619356"
],
"output_participant_list": [
"R-MMU-5619396"
],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619425",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619425"
}
]
},
{
"id": "R-MMU-5619428",
"name": "Egr2 activates Hoxa2 chromatin",
"equation": "",
"summary": "Hoxa2 expression in embryos is driven by Egr2 (Krox20) in rhombomeres 3 and 5 (r3, r5) (Maconochie et al. 2001) and by Hoxb1 in r4 (Tumpel et al. 2007, Lampe et al. 2008). Egr2 binds sites in the 5' region of the Hoxa2 gene (Maconochie et al.2001). (Hoxa2 is the only Hox gene active in r2 (Lampe et al 2004). An unknown activator, possibly a transcription factor of the Sox family, may be involved in expression in r2 (Tumpel et al. 2008)).",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"P08152-1",
"P08775-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619428",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619428"
}
]
},
{
"id": "R-MMU-5619430",
"name": "Egr2 (Krox20) activates Hoxb2 expression",
"equation": "",
"summary": "Egr2 (Krox20) binds three sites in the 5' region of the Hoxb2 gene and activates expression in rhombomere 3 (r3) and r5 (Sham et al. 1993, Maconochie et al. 2001, Ferrai et al. 2009). Hoxb1 activates Hoxb2 in r4 and expression is also observed in r6 and r7.",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08152-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619430",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619430"
}
]
},
{
"id": "R-MMU-5619432",
"name": "Hoxb2 gene is transcribed",
"equation": "",
"summary": "The Hoxb2 gene is transcribed to yield mRNA (Rubock et al. 1990, Sham et al. 1993, Vesque et al. 1996, Maconochie et al. 1997, Jacobs et al. 1999, Ferretti et al. 2000, Maconochie et al. 2001, Ferrai et al. 2009). Hoxb2 mRNA is observed in rhombomere 3 and caudally in the neural tube and mesoderm derivatives such as lung (Rubock et al. 1990).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5619364"
],
"output_participant_list": [
"R-MMU-5619339"
],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08152-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619432",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619432"
}
]
},
{
"id": "R-MMU-5619434",
"name": "Retinoic acid activates Hoxa4 chromatin",
"equation": "",
"summary": "In mouse embryos retinoic acid initially activates expression of the Hoxa4 gene in rhombomere 7 (r7) and regions of mesoderm 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 (Behringer et al. 1993, Morrison et al. 1997, Packer et al. 1998, Packer et al. 2000), causing dissociation of corepressors and recruitment of corepressors (inferred from Hoxa1, Gillespie and Gudas 2007, Kashyap and Gudas 2010). Hoxa4 itself maintains later expression in an autoregulatory loop (Wu and Wolgemuth 1993, Packer et al. 1998).
Treatment of embryonic stem cells with retinoic acid causes loss of methylation at histone 3 lysine-27 (H3K27me3, Kashyap et al. 2011, Mazzoni et al. 2013, Shpargel et al. 2014), loss of Polycomb repressive complex 2 (PRC2, Mazzoni et al. 2013) and gain of methylation at histone 3 lysine-4 (H3K4me3, Kashyap et al. 2011) across the Hoxa gene cluster. The Mll2 complex methylates H3K4 at Hoxa4 in fibroblasts (Wang et al. 2009).",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"O09000-1",
"Q61188-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619434",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619434"
}
]
},
{
"id": "R-MMU-5619435",
"name": "Hoxb3 gene is transcribed",
"equation": "",
"summary": "The Hoxb3 gene is transcribed to yield mRNA (Sham et al. 1992, Manzanares et al. 1997, Manzanares et al. 2002, Yau et al. 2002, Mechta-Grigoriou et al. 2003). Hoxb3 mRNA is observed strongly in rhombomere 5 (Manzanares et al. 1997, Manzanares et al. 2002) and more weakly in rhombomeres 6 and 7 of the hindbrain (Kwan et al. 2001, Yau et al. 2002). Hoxb3 mRNA is also observed in mesodermal derivatives including lung, stomach, pancreas, and metanephros, and in neural crest derivatives (Sham et al. 1992).",
"cellular_location": "cytosol, nucleoplasm",
"input_participant_list": [
"R-MMU-5619351"
],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08152-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619435",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619435"
}
]
},
{
"id": "R-MMU-5619436",
"name": "Hoxc4 chromatin is activated",
"equation": "",
"summary": "Hoxc4 is expressed in embryos at E12.5 caudal to rhombomere 7 (r7, Geada et al. 1992). Hoxc4 is also expressed at the level of prevertebrae 4-5, in spinal column, esophagus, lung, trachea, and metanephric kidney (Geada et al. 1992). Vitamin A (and hence retinoic acid) appears to induce expression of Hoxc4 (Liu and Zhu 2000). Hoxc4 is induced by beta-catenin during neurogenesis of embryonic stem cells (Otero et al. 2004). 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) during treatment of embryonic stem cells with retinoic acid (Mazzoni et al. 2013).",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"Q61188-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619436",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619436"
}
]
},
{
"id": "R-MMU-5619437",
"name": "Hoxd3 chromatin is activated",
"equation": "",
"summary": "Retinoic acid induces expression of Hoxd3 in embryos (Folberg et al. 1999) and fetal cortical neurons (Chai et al. 2009), but it is unknown if the effect is direct or indirect. The retinoid receptor Rarb is not responsible for the inducibility in embryos (Folberg et al. 1999). Hoxd3 is expressed in rhombomeres 5,6, and 7 (r5-7) (Tan et al. 1996, Gaufo et al. 2003) and in more caudal regions: the spinal cord, dorsal root ganglia, first cervical vertebrae, thyroid gland, kidney tublules, esophagus, stomach, and intestines (Tan et al. 1996).
In mouse embryonic stem cells treated with retinoic acid Hoxd3 chromatin is activated by loss of methylation at lysine-27 of histone H3 (H3K27me3) and loss of Polycomb repressive complex 2 (PRC2) (Williamson et al. 2012, Mazzoni et al. 2013). In human fibroblasts, the histone demethylase KDM6A participates in removing H3K27me3. The Mll2 complex methylates H3K4 at Hoxd3 in fibroblasts (Wang et al. 2009).",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"Q61188-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619437",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619437"
}
]
},
{
"id": "R-MMU-5619440",
"name": "Mafb:Jun and Egr2 activate Hoxb3 expression",
"equation": "",
"summary": "During embryogenesis 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 (Manzanares et al. 1997, Manzanares et al. 1999, Manzanares et al. 2002, Yau et al. 2002, Mechta-Grigoriou et al. 2003). Egr2 (Krox20) also binds the r5 enhancer and is required to activate the Hoxb3 gene in r5 (Manzanares et al. 2002). After initial activation Hoxb3 is hypothesized to maintain its own expression (Yau et al. 2002). Hoxb3 is expressed most strongly in r5 and more weakly in caudal rhombomeres r6 and r7.",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08152-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619440",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619440"
}
]
},
{
"id": "R-MMU-5619441",
"name": "Retinoic acid activates Hoxd4 chromatin",
"equation": "",
"summary": "Retinoic acid activates the Hoxd4 gene in rhombomere 7 (r7) of embryos by binding Rarb (Folberg et al. 1999, Serpente et al. 2005), Rara, or Rarg (Wendling et al. 2001) in Rar:Rxr receptor dimers bound to a retinoic acid response element (RARE) in the 5' flanking region of the gene (Popperl and Featherstone 1993, Folberg et al. 1997, Zhang et al. 1997, Zhang et al. 2000, Wendling et al. 2001, Nolte et al. 2003). Ligand binding by retinoic acid receptors causes dismissal of corepressors such as Ncor1 and recruitment of coactivators such as Ncoa3 (Horlein et al. 1995, inferred from Hoxa1 in Gillespie and Gudas 2007, Kashyap and Gudas 2010). Pax6 binds near the RARE and is required for maximal activation (Nolte et al. 2006).
Activation of chromatin at Hoxd4 is accompanied by loss of methylation at lysine-27 (H3K27me3) and gain of H3K4me3 (Rastegar et al. 2012, Williamson et al. 2012, Mazzoni et al. 2013). The Mll2 complex methylates H3K4 at Hoxd4 in fibroblasts (Wang et al. 2009). In human cells the histone demethylase KDM6A (UTX) binds HOXD4 and may participate in demethylating H3K27me3. Other factors may also be involved in histone demethylation. Polycomb repressive complex 2 (PRC2), which binds H3K27me3, and Pcgf2 (Mel18) also dissociate (Kobrossy et al. 2006, Mazzoni et al. 2013). YY1, however, remains associated even after treatment with retinoic acid (Kobrossy et al. 2006). After activation by retinoic acid, Hoxd4 maintains its own expression by binding and activating its own promoter (Kobrossy et al. 2006).",
"cellular_location": "nucleoplasm",
"input_participant_list": [
"R-MMU-187295"
],
"output_participant_list": [
"R-MMU-5619463"
],
"enzyme_list": [
"B2RWS6-1",
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"O09000-1",
"P45481-1",
"Q61188-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5619441",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5619441"
}
]
},
{
"id": "R-MMU-5621004",
"name": "Hoxb1 activates Hoxb2 expression",
"equation": "",
"summary": "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) of embryos (Maconochie et al. 1997, Jacobs et al. 1999, Ferretti et al. 2000, Ferrai et al. 2009). Egr2 (Krox20) activates Hoxb2 in r3 and r5 and expression is also observed in r6 and r7.",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5621004",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5621004"
}
]
},
{
"id": "R-MMU-5621012",
"name": "Hoxb1 activates Hoxa2 expression",
"equation": "",
"summary": "Hoxa2 expression is driven by Hoxb1 in rhombomere 4 (r4) (Tumpel et al. 2007, Lampe et al. 2008) and Egr2 (Krox20) in r3 and r5 (Maconochie et al. 2001). Hoxb1 together with Pbx and Prep/Meis cofactors bind an element in the intron of Hoxa2 (Tumpel et al. 2007, Lampe et al. 2008, Tumpel et al. 2008). Hoxa2 also autoregulates in r4 (Tumpel et al. 2007, Lampe et al. 2008). (Hoxa2 is the only Hox gene active in r2 (Lampe et al 2004). An unknown activator, possibly a transcription factor of the Sox family, may be involved in expression in r2 (Tumpel et al. 2008)).",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"O70546-1",
"Q6PDK2-1",
"P08775-1",
"Q8BRH4-1",
"Q8CFI7-1"
],
"evidence": [
{
"id": "R-MMU-5621012",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5621012"
}
]
},
{
"id": "R-MMU-5661121",
"name": "KDM6A, KDM6B, KDM7A demethylate Me3K28-histone H3",
"equation": "",
"summary": "This event has been computationally inferred from an event that has been demonstrated in another species.
The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.
More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp", "cellular_location": "nucleoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "P79457-1", "Q5NCY0-1", "O70546-1", "Q3UWM4-1" ], "evidence": [ { "id": "R-MMU-5661121", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5661121" } ] }, { "id": "R-MMU-5693628", "name": "Hoxb1 maintains activation of Hoxb1 chromatin", "equation": "", "summary": "In mouse embryos (Ferretti et al. 2000) and embryonal carcinoma cells (Ferretti et al. 2000, Ferretti et al. 2005), Hoxb1 binds with the Pbx1:Pknox1 (Pbx1:Prep1) heterodimer and Meis1 (Huang et al. 2005) at 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 appears to positively regulate HOXB1 transcription (Di Rocco et al. 2001).", "cellular_location": "nucleoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "B2RWS6-1", "O70546-1", "Q6PDK2-1", "P08775-1", "Q8BRH4-1", "O09000-1", "Q8CFI7-1" ], "evidence": [ { "id": "R-MMU-5693628", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-MMU-5693628" } ] }, { "id": "R-MMU-6810138", "name": "Hoxa2 chromatin is activated", "equation": "", "summary": "As inferred from mouse embryonic stem cells activated by retinoic acid (Kashyap et al. 2011, Mazzoni et al. 2013, Shpargel et al. 2014) and human cell lines, activation of Hoxa2 chromatin is accompanied by loss of methylation at lysine-27 of histone H3 (H3K27, Kashyap et al. 2011, Mazzoni et al. 2013, Shpargel et al. 2014), dissociation of polycomb repressive complexes (Mazzoni et al. 2013), and gain of methylation at H3K4 (Kashyap et al. 2011). The histone demethylase Kdm6a and possibly other factors (Shpargel et al. 2014) may participate in removing H3K27 methylation. The Mll2 complex methylates H3K4 at Hoxa2 in fibroblasts (Wang et al. 2009).", "cellular_location": "nucleoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "O70546-1", "Q61188-1" ], "evidence": [ { "id": "R-MMU-6810138", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-MMU-6810138" } ] }, { "id": "R-MMU-6810150", "name": "Hoxb3 chromatin is activated", "equation": "", "summary": "As inferred from mouse embryonic stem cells activated by retinoic acid (Kashyap et al. 2011, Mazzoni et al. 2013) and human cells, activation of chromatin at Hoxb3 is accompanied by loss of methylation at lysine-27 of histone H3 (H3K27me3, Kashyap et al. 2011, Mazzoni et al. 2013), loss of PRC2 (Mazzoni et al. 2013), and gain of methylation at H3K4 (Kashyap et al. 2011). The Mll2 complex methylates H3K4 at Hoxb3 in fibroblasts (Wang et al. 2009). In human cells the demethylase KDM6A (UTX) binds HOXB3 chromatin during activation and participates in demethylating H3K27me3.", "cellular_location": "nucleoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "O70546-1", "Q6PDK2-1", "Q8BRH4-1", "Q61188-1" ], "evidence": [ { "id": "R-MMU-6810150", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-MMU-6810150" } ] }, { "id": "R-MMU-6810169", "name": "Hoxa3 chromatin is activated", "equation": "", "summary": "As inferred from mouse embryonic stem cells (Kashyap et al. 2011, Mazzoni et al. 2013) and embryos (Diman et al. 2011) activated by retinoic acid and human fibroblasts and embryonal carcinoma cells, Hoxa3 chromatin is activated by loss of methylation at lysine-27 of histone H3 (H3K27me3, Kashyap et al. 2011, Mazzoni et al. 2013). loss of Polycomb repressive complex (PRC2, Mazzoni et al. 2013), and gain of H3K4me3 (Kashyap et al. 2011). The Mll2 complex methylates H3K4 at Hoxa3 in fibroblasts (Wang et al. 2009). In human cells KDM6A (UTX) binds HOXA3 and participates in the loss of H3K27me3.", "cellular_location": "nucleoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "O70546-1", "Q6PDK2-1", "Q8BRH4-1", "Q61188-1" ], "evidence": [ { "id": "R-MMU-6810169", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-MMU-6810169" } ] }, { "id": "R-MMU-6810170", "name": "Hoxb2 chromatin is activated", "equation": "", "summary": "As inferred from mouse embryonic stem cells activated by retinoic acid (Kashyap et al. 2011, Mazzoni et al. 2013) and human cell lines, methylation at lysine-27 of histone H3 (H3K27me3) is lost (Kashyap et al. 2011, Mazzoni et al. 2013), Polycomb repressive complex 2 (PRC2) is lost (Mazzoni et al. 2013), and methylation at lysine-4 (H3K4me3) is gained (Kashyap et al. 2011). The Mll2 complex methylates H3K4 at Hoxb2 in fibroblasts (Wang et al. 2009). In human cells, the histone demethylase KDM6A (UTX) binds HOXB2 chromatin and demethylates H3K27me3. Other factors may also participate in demethylation.", "cellular_location": "nucleoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "O70546-1", "Q6PDK2-1", "Q8BRH4-1", "Q61188-1" ], "evidence": [ { "id": "R-MMU-6810170", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-MMU-6810170" } ] }, { "id": "R-MMU-9821410", "name": "PAXIP1:PAGR1 complex, NCOA6 and KDM6A bind MLL4 complex", "equation": "", "summary": "This event has been computationally inferred from an event that has been demonstrated in another species.
The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.
More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp", "cellular_location": "nucleoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "O70546-1", "Q6PDK2-1" ], "evidence": [ { "id": "R-MMU-9821410", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-MMU-9821410" } ] }, { "id": "R-MMU-9821412", "name": "PAXIP1:PAGR1 complex, NCOA6 and KDM6A bind MLL3 complex", "equation": "", "summary": "This event has been computationally inferred from an event that has been demonstrated in another species.
The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.
More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp", "cellular_location": "nucleoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "O70546-1", "Q8BRH4-1" ], "evidence": [ { "id": "R-MMU-9821412", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-MMU-9821412" } ] }, { "id": "R-MMU-9822964", "name": "Kdm6a (Utx) demethylates trimethylated histone H3 lysine-27 (H3K27me3)", "equation": "", "summary": "Kdm6a (UTX) demethylates histone H3 trimethyllysine-27 (H3K27me3, lysine-28 of the preprotein) to yield histone H3 monomethyllysine-27 (H3K27me1) (inferred from the human homolog). Kdm6a participates in demethylating genome-wide H3K27me3 in cleavage stage embryos (Bai et al. 2019).", "cellular_location": "nucleoplasm", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "O70546-1" ], "evidence": [ { "id": "R-MMU-9822964", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-MMU-9822964" } ] } ], "reaction_participants": [ { "participant_id": "R-ALL-5334804", "participant_name": "atRA [nucleoplasm]", "crossref": [ { "id": "C00777", "database": "COMPOUND", "url": "" }, { "id": "HMDB0001852", "database": "HMDB Metabolite", "url": "" }, { "id": "15367", "database": "ChEBI", "url": "" }, { "id": "000012358651", "database": "ZINC", "url": "" }, { "id": "2644", "database": "Guide to Pharmacology - Ligands", "url": "" }, { "id": "000012358651", "database": "ZINC", "url": "" }, { "id": "2644", "database": "Guide to Pharmacology - Ligands", "url": "" }, { "id": "15367", "database": "ChEBI", "url": "" }, { "id": "C00777", "database": "COMPOUND", "url": "" }, { "id": "HMDB0001852", "database": "HMDB Metabolite", "url": "" } ] }, { "participant_id": "R-MMU-187295", "participant_name": "Pax6 [nucleoplasm]", "crossref": [ { "id": "NP_001231130.1", "database": "RefSeq", "url": "" }, { "id": "ENSMUST00000111087", "database": "Ensembl", "url": "" }, { "id": "P63015", "database": "PRO", "url": "" }, { "id": "ENSMUSG00000027168", "database": "Ensembl", "url": "" }, { "id": "ENSMUSP00000087870", "database": "Ensembl", "url": "" }, { "id": "ENSMUSP00000106715", "database": "Ensembl", "url": "" }, { "id": "HMDBP13574", "database": "HMDB Protein", "url": "" }, { "id": "ENSMUST00000090397", "database": "Ensembl", "url": "" }, { "id": "ENSMUST00000111085", "database": "Ensembl", "url": "" }, { "id": "NP_001297074.1", "database": "RefSeq", "url": "" }, { "id": "ENSMUSP00000129344", "database": "Ensembl", "url": "" }, { "id": "ENSMUSP00000087878", "database": "Ensembl", "url": "" }, { "id": "ENSMUST00000111082", 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"start_pos", "end_pos", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 3 } ], "sort_fields": [ "start_pos", "end_pos", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 17 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }