Gene Expression Literature Summary

• Symbol: Hoxd9
• Name: homeobox D9
• ID: MGI:96210

80 matching records from 80 references.

Summary by Age and Assay: Numbers in the table indicate the number of results matching the search criteria.

Age	E1.5	E2	E8	E8.5	E9	E9.5	E10	E10.5	E11	E11.5	E12	E12.5	E13	E13.5	E14	E14.5	E15	E15.5	E16	E16.5	E17	E17.5	E18.5	E19.5	E	P
Immunohistochemistry (section)										1																1
In situ RNA (section)				3	3	4	2	4		1	1	15	1	4	1	5	1	3			1	2	1			6
In situ RNA (whole mount)			1		3	9		20	3	11	2	15	2	2				1				1			3
In situ reporter (knock in)						1		1	1	1	1														1
Northern blot									1
RT-PCR	1	1		2	1	5		3	1	4		7	1	4		2	2	1	1	2	1	1	2	1		6
cDNA clones				1			1																			1
Nuclease S1									1

Summary by Gene and Reference: Number indicates the number of results matching the search criteria recorded for each reference.
* Indicates detailed expression data entries available

Hoxd9  homeobox D9   (Synonyms: Hox-4.4, Hox-5.2)
Results	Reference
3	J:319862 Amandio AR, Beccari L, Lopez-Delisle L, Mascrez B, Zakany J, Gitto S, Duboule D, Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster. Genes Dev. 2021 Nov 1;35(21-22):1490-1509
2	J:62547 Barna M, Hawe N, Niswander L, Pandolfi PP, Plzf regulates limb and axial skeletal patterning. Nat Genet. 2000 Jun;25(2):166-72
1	J:99990 Barna M, Pandolfi PP, Niswander L, Gli3 and Plzf cooperate in proximal limb patterning at early stages of limb development. Nature. 2005 Jul 14;436(7048):277-81
1	J:283343 Bastida MF, Perez-Gomez R, Trofka A, Zhu J, Rada-Iglesias A, Sheth R, Stadler HS, Mackem S, Ros MA, The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13. Proc Natl Acad Sci U S A. 2020 Jan 14;117(2):1090-1096
1	J:200262 Bobick BE, Cobb J, Shox2 regulates progression through chondrogenesis in the mouse proximal limb. J Cell Sci. 2012 Dec 15;125(Pt 24):6071-83
1	J:326458 Bolt CC, Lopez-Delisle L, Hintermann A, Mascrez B, Rauseo A, Andrey G, Duboule D, Context-dependent enhancer function revealed by targeted inter-TAD relocation. Nat Commun. 2022 Jun 17;13(1):3488
1	J:308920 Bolt CC, Lopez-Delisle L, Mascrez B, Duboule D, Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations. Nat Commun. 2021 Aug 18;12(1):5013
4*	J:23135 Burke AC, Nelson CE, Morgan BA, Tabin C, Hox genes and the evolution of vertebrate axial morphology. Development. 1995 Feb;121(2):333-46
1	J:109528 Capellini TD, Di Giacomo G, Salsi V, Brendolan A, Ferretti E, Srivastava D, Zappavigna V, Selleri L, Pbx1/Pbx2 requirement for distal limb patterning is mediated by the hierarchical control of Hox gene spatial distribution and Shh expression. Development. 2006 Jun;133(11):2263-73
1*	J:139570 Capellini TD, Zewdu R, Di Giacomo G, Asciutti S, Kugler JE, Di Gregorio A, Selleri L, Pbx1/Pbx2 govern axial skeletal development by controlling Polycomb and Hox in mesoderm and Pax1/Pax9 in sclerotome. Dev Biol. 2008 Sep 15;321(2):500-14
1*	J:44765 Carpenter EM, Goddard JM, Davis AP, Nguyen TP, Capecchi MR, Targeted disruption of Hoxd-10 affects mouse hindlimb development. Development. 1997 Nov;124(22):4505-14
1	J:29274 Chan DC, Wynshaw-Boris A, Leder P, Formin isoforms are differentially expressed in the mouse embryo and are required for normal expression of fgf-4 and shh in the limb bud. Development. 1995 Oct;121(10):3151-62
3*	J:52279 Chen F, Capecchi MR, Paralogous mouse Hox genes, Hoxa9, Hoxb9, and Hoxd9, function together to control development of the mammary gland in response to pregnancy. Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):541-6
1	J:342014 Chen Y, Zhou T, Liao Z, Gao W, Wu J, Zhang S, Li Y, Liu H, Zhou H, Xu C, Su P, Hnrnpk is essential for embryonic limb bud development as a transcription activator and a collaborator of insulator protein Ctcf. Cell Death Differ. 2023 Oct;30(10):2293-2308
4*	J:119560 Choi MY, Romer AI, Hu M, Lepourcelet M, Mechoor A, Yesilaltay A, Krieger M, Gray PA, Shivdasani RA, A dynamic expression survey identifies transcription factors relevant in mouse digestive tract development. Development. 2006 Oct;133(20):4119-29
3	J:299212 Coughlan E, Garside VC, Wong SFL, Liang H, Kraus D, Karmakar K, Maheshwari U, Rijli FM, Bourne J, McGlinn E, A Hox Code Defines Spinocerebellar Neuron Subtype Regionalization. Cell Rep. 2019 Nov 19;29(8):2408-2421.e4
2	J:277177 Darbellay F, Bochaton C, Lopez-Delisle L, Mascrez B, Tschopp P, Delpretti S, Zakany J, Duboule D, The constrained architecture of mammalian Hox gene clusters. Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13424-13433
3	J:203785 Delpretti S, Montavon T, Leleu M, Joye E, Tzika A, Milinkovitch M, Duboule D, Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding. Cell Rep. 2013 Oct 17;5(1):137-50
2	J:131874 Di-Poi N, Zakany J, Duboule D, Distinct Roles and Regulations for Hoxd Genes in Metanephric Kidney Development. PLoS Genet. 2007 Dec 21;3(12):e232
1*	J:153498 Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nurnberger A, SchmidtK, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini MA, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, et al., A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol. 2011;9(1):e1000582
6*	J:122527 Dolle P, Duboule D, Two gene members of the murine HOX-5 complex show regional and cell-type specific expression in developing limbs and gonads. EMBO J. 1989 May;8(5):1507-15
2*	J:1778 Dolle P, Izpisua-Belmonte JC, Boncinelli E, Duboule D, The Hox-4.8 gene is localized at the 5' extremity of the Hox-4 complex and is expressed in the most posterior parts of the body during development. Mech Dev. 1991 Dec;36(1-2):3-13
6	J:37004 Dolle P, Izpisua-Belmonte JC, Brown JM, Tickle C, Duboule D, HOX-4 genes and the morphogenesis of mammalian genitalia. Genes Dev. 1991 Oct;5(10):1767-7
6*	J:21265 Dolle P, Izpisua-Belmonte JC, Falkenstein H, Renucci A, Duboule D, Coordinate expression of the murine Hox-5 complex homoeobox-containing genes during limb pattern formation. Nature. 1989 Dec 14;342(6251):767-72
3*	J:15802 Duboule D, The function of Hox genes in the morphogenesis of the vertebrate limb. Ann Genet. 1993;36(1):24-9
2*	J:9951 Duboule D, Dolle P, The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. EMBO J. 1989 May;8(5):1497-505
1*	J:128903 Feng W, Huang J, Zhang J, Williams T, Identification and analysis of a conserved Tcfap2a intronic enhancer element required for expression in facial and limb bud mesenchyme. Mol Cell Biol. 2008 Jan;28(1):315-25
3*	J:328711 Fernandez-Guerrero M, Zdral S, Castilla-Ibeas A, Lopez-Delisle L, Duboule D, Ros MA, Time-sequenced transcriptomes of developing distal mouse limb buds: A comparative tissue layer analysis. Dev Dyn. 2022 Sep;251(9):1550-1575
3*	J:46439 Freeman TC, Dixon AK, Campbell EA, Tait TM, Richardson PJ, Rice KM, Maslen GL, Metcalfe AD, Streuli CH, Bentley DR, Expression Mapping of Mouse Genes. MGI Direct Data Submission. 1998;
5*	J:149067 Grier DG, Thompson A, Lappin TR, Halliday HL, Quantification of Hox and Surfactant Protein-B Transcription during Murine Lung Development. Neonatology. 2009 Feb 10;96(1):50-60
1*	J:171409 GUDMAP Consortium, GUDMAP: the GenitoUrinary Development Molecular Anatomy Project. www.gudmap.org. 2004;
2	J:88217 Hedlund E, Karsten SL, Kudo L, Geschwind DH, Carpenter EM, Identification of a Hoxd10-regulated transcriptional network and combinatorial interactions with Hoxa10 during spinal cord development. J Neurosci Res. 2004 Feb 1;75(3):307-19
3	J:308865 Higashijima Y, Nagai N, Yamamoto M, Kitazawa T, Kawamura YK, Taguchi A, Nakada N, Nangaku M, Furukawa T, Aburatani H, Kurihara H, Wada Y, Kanki Y, Lysine demethylase 7a regulates murine anterior-posterior development by modulating the transcription of Hox gene cluster. Commun Biol. 2020 Nov 30;3(1):725
2*	J:326160 Hintermann A, Guerreiro I, Lopez-Delisle L, Bolt CC, Gitto S, Duboule D, Beccari L, Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken. Development. 2022 Jun 15;149(12):dev200594
1*	J:69781 Ikeya M, Takada S, Wnt-3a is required for somite specification along the anteroposterior axis of the mouse embryo and for regulation of cdx-1 expression. Mech Dev. 2001 May;103(1-2):27-33
1*	J:11135 Izpisua-Belmonte JC, Dolle P, Renucci A, Zappavigna V, Falkenstein H, Duboule D, Primary structure and embryonic expression pattern of the mouse Hox-4.3 homeobox gene. Development. 1990 Nov;110(3):733-45
4*	J:32046 Izpisua-Belmonte JC, Falkenstein H, Dolle P, Renucci A, Duboule D, Murine genes related to the Drosophila AbdB homeotic genes are sequentially expressed during development of the posterior part of the body. EMBO J. 1991 Aug;10(8):2279-89
2	J:232412 Jeon S, Seong RH, Anteroposterior Limb Skeletal Patterning Requires the Bifunctional Action of SWI/SNF Chromatin Remodeling Complex in Hedgehog Pathway. PLoS Genet. 2016 Mar;12(3):e1005915
1	J:166088 Jung H, Lacombe J, Mazzoni EO, Liem KF Jr, Grinstein J, Mahony S, Mukhopadhyay D, Gifford DK, Young RA, Anderson KV, Wichterle H, Dasen JS, Global control of motor neuron topography mediated by the repressive actions of a single hox gene. Neuron. 2010 Sep 9;67(5):781-96
5	J:238554 Kaminski MM, Tosic J, Kresbach C, Engel H, Klockenbusch J, Muller AL, Pichler R, Grahammer F, Kretz O, Huber TB, Walz G, Arnold SJ, Lienkamp SS, Direct reprogramming of fibroblasts into renal tubular epithelial cells by defined transcription factors. Nat Cell Biol. 2016 Dec;18(12):1269-1280
2*	J:22469 Kanzler B, Viallet JP, Le Mouellic H, Boncinelli E, Duboule D, Dhouailly D, Differential expression of two different homeobox gene families during mouse tegument morphogenesis. Int J Dev Biol. 1994 Dec;38(4):633-40
16	J:54386 Khoa ND, Hasunuma T, Kobata T, Kato T, Nishioka K, Expression of murine HOXD9 during embryonic joint patterning and in human T lymphotropic virus type I tax transgenic mice with arthropathy resembling rheumatoid arthritis. Arthritis Rheum. 1999 Apr;42(4):686-96
1	J:338694 Kumar S, Alam SS, Bareke E, Beauchamp MC, Dong Y, Chan W, Majewski J, Jerome-Majewska LA, Sf3b4 regulates chromatin remodeler splicing and Hox expression. Differentiation. 2023 May-Jun;131:59-73
2	J:66266 Lewandoski M, Sun X, Martin GR, Fgf8 signalling from the AER is essential for normal limb development. Nat Genet. 2000 Dec;26(4):460-3
6	J:124112 McIntyre DC, Rakshit S, Yallowitz AR, Loken L, Jeannotte L, Capecchi MR, Wellik DM, Hox patterning of the vertebrate rib cage. Development. 2007 Aug;134(16):2981-9
2	J:131545 Montavon T, Le Garrec JF, Kerszberg M, Duboule D, Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbness. Genes Dev. 2008 Feb 1;22(3):346-59
1	J:228776 Muto A, Ikeda S, Lopez-Burks ME, Kikuchi Y, Calof AL, Lander AD, Schilling TF, Nipbl and mediator cooperatively regulate gene expression to control limb development. PLoS Genet. 2014 Sep;10(9):e1004671
4	J:247259 Naruse C, Shibata S, Tamura M, Kawaguchi T, Abe K, Sugihara K, Kato T, Nishiuchi T, Wakana S, Ikawa M, Asano M, New insights into the role of Jmjd3 and Utx in axial skeletal formation in mice. FASEB J. 2017 Jun;31(6):2252-2266
4	J:217206 Neufeld SJ, Wang F, Cobb J, Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb. Genetics. 2014 Nov;198(3):1117-26
1	J:283357 Nowotschin S, Setty M, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis AK, Pe'er D, The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature. 2019 May;569(7756):361-367
4*	J:89197 Patterson LT, Potter SS, Atlas of Hox gene expression in the developing kidney. Dev Dyn. 2004 Apr;229(4):771-9
1*	J:43311 Peichel CL, Prabhakaran B, Vogt TF, The mouse Ulnaless mutation deregulates posterior HoxD gene expression and alters appendicular patterning. Development. 1997 Sep;124(18):3481-92
2	J:198638 Raines AM, Adam M, Magella B, Meyer SE, Grimes HL, Dey SK, Potter SS, Recombineering-based dissection of flanking and paralogous Hox gene functions in mouse reproductive tracts. Development. 2013 Jul;140(14):2942-52
5*	J:130 Renucci A, Zappavigna V, Zakany J, Izpisua-Belmonte JC, Burki K, Duboule D, Comparison of mouse and human HOX-4 complexes defines conserved sequences involved in the regulation of Hox-4.4. EMBO J. 1992 Apr;11(4):1459-68
3	J:118803 Ribes V, Otto DM, Dickmann L, Schmidt K, Schuhbaur B, Henderson C, Blomhoff R, Wolf CR, Tickle C, Dolle P, Rescue of cytochrome P450 oxidoreductase (Por) mouse mutants reveals functions in vasculogenesis, brain and limb patterning linked to retinoic acid homeostasis. Dev Biol. 2007 Mar 1;303(1):66-81
2	J:299264 Rodriguez-Carballo E, Lopez-Delisle L, Willemin A, Beccari L, Gitto S, Mascrez B, Duboule D, Chromatin topology and the timing of enhancer function at the HoxD locus. Proc Natl Acad Sci U S A. 2020 Dec 8;117(49):31231-31241
1*	J:336421 Rodriguez-Carballo E, Lopez-Delisle L, Yakushiji-Kaminatsui N, Ullate-Agote A, Duboule D, Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes. BMC Biol. 2019 Jul 12;17(1):55
1	J:290220 Sato T, Kataoka K, Ito Y, Yokoyama S, Inui M, Mori M, Takahashi S, Akita K, Takada S, Ueno-Kudoh H, Asahara H, Lin28a/let-7 pathway modulates the Hox code via Polycomb regulation during axial patterning in vertebrates. Elife. 2020 May 29;9:e53608
3	J:239094 Schep R, Necsulea A, Rodriguez-Carballo E, Guerreiro I, Andrey G, Nguyen Huynh TH, Marcet V, Zakany J, Duboule D, Beccari L, Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7720-E7729
2*	J:172713 Schorderet P, Duboule D, Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet. 2011 May;7(5):e1002071
2*	J:71996 Selleri L, Depew MJ, Jacobs Y, Chanda SK, Tsang KY, Cheah KS, Rubenstein JL, O'Gorman S, Cleary ML, Requirement for Pbx1 in skeletal patterning and programming chondrocyte proliferation and differentiation. Development. 2001 Sep;128(18):3543-57
2*	J:204375 Sheth R, Bastida MF, Kmita M, Ros M, "Self-regulation," a new facet of Hox genes' function. Dev Dyn. 2014 Jan;243(1):182-91
1	J:128015 Sheth R, Bastida MF, Ros M, Hoxd and Gli3 interactions modulate digit number in the amniote limb. Dev Biol. 2007 Oct 15;310(2):430-41
4*	J:209112 Shimizu H, Kubo A, Uchibe K, Hashimoto M, Yokoyama S, Takada S, Mitsuoka K, Asahara H, The AERO system: a 3D-like approach for recording gene expression patterns in the whole mouse embryo. PLoS One. 2013;8(10):e75754
1*	J:100233 Shou S, Scott V, Reed C, Hitzemann R, Stadler HS, Transcriptome analysis of the murine forelimb and hindlimb autopod. Dev Dyn. 2005 Sep;234(1):74-89
1	J:169050 Soshnikova N, Montavon T, Leleu M, Galjart N, Duboule D, Functional analysis of CTCF during mammalian limb development. Dev Cell. 2010 Dec 14;19(6):819-30
1*	J:43764 Takihara Y, Tomotsune D, Shirai M, Katoh-Fukui Y, Nishii K, Motaleb MA , Nomura M , Tsuchiya R , Fujita Y , Shibata Y , Higashinakagawa T , Shimada K, Targeted disruption of the mouse homologue of the Drosophila polyhomeotic gene leads to altered anteroposterior patterning and neural crest defects. Development. 1997 Oct;124(19):3673-82
2*	J:174767 Tang F, Barbacioru C, Nordman E, Bao S, Lee C, Wang X, Tuch BB, Heard E, Lao K, Surani MA, Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS One. 2011;6(6):e21208
2	J:105255 Tarchini B, Duboule D, Control of Hoxd genes' collinearity during early limb development. Dev Cell. 2006 Jan;10(1):93-103
1	J:182758 Tschopp P, Christen AJ, Duboule D, Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters. Development. 2012 Mar;139(5):929-39
5	J:146752 Tschopp P, Tarchini B, Spitz F, Zakany J, Duboule D, Uncoupling time and space in the collinear regulation of Hox genes. PLoS Genet. 2009 Mar;5(3):e1000398
1	J:130489 Wu Y, Wang G, Scott SA, Capecchi MR, Hoxc10 and Hoxd10 regulate mouse columnar, divisional and motor pool identity of lumbar motoneurons. Development. 2008 Jan;135(1):171-82
2	J:170090 Xu B, Wellik DM, Axial Hox9 activity establishes the posterior field in the developing forelimb. Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4888-91
1	J:89029 Yashiro K, Zhao X, Uehara M, Yamashita K, Nishijima M, Nishino J, Saijoh Y, Sakai Y, Hamada H, Regulation of retinoic acid distribution is required for proximodistal patterning and outgrowth of the developing mouse limb. Dev Cell. 2004 Mar;6(3):411-22
3*	J:156017 Yokoyama S, Ito Y, Ueno-Kudoh H, Shimizu H, Uchibe K, Albini S, Mitsuoka K, Miyaki S, Kiso M, Nagai A, Hikata T, Osada T, Fukuda N, Yamashita S, Harada D, Mezzano V, Kasai M, Puri PL, Hayashizaki Y, Okado H, Hashimoto M, Asahara H, A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Dev Cell. 2009 Dec;17(6):836-48
1	J:127046 Zacchetti G, Duboule D, Zakany J, Hox gene function in vertebrate gut morphogenesis: the case of the caecum. Development. 2007 Nov;134(22):3967-3973
1	J:225113 Zhang Y, Liu Z, Medrzycki M, Cao K, Fan Y, Reduction of Hox gene expression by histone H1 depletion. PLoS One. 2012;7(6):e38829
1	J:170604 Zhang Z, O'Rourke JR, McManus MT, Lewandoski M, Harfe BD, Sun X, The microRNA-processing enzyme Dicer is dispensable for somite segmentation but essential for limb bud positioning. Dev Biol. 2011 Mar 15;351(2):254-65
1	J:200718 Zhou W, Zhu H, Zhao J, Li H, Wan Y, Cao J, Zhao H, Yu J, Zhou R, Yao Y, Zhang L, Wang L, He L, Ma G, Yao Z, Guo X, Misexpression of Pknox2 in mouse limb bud mesenchyme perturbs zeugopod development and deltoid crest formation. PLoS One. 2013;8(5):e64237
1*	J:187603 Zhu H, Zhao J, Zhou W, Li H, Zhou R, Zhang L, Zhao H, Cao J, Zhu X, Hu H, Ma G, He L, Yao Z, Yao L, Guo X, Ndrg2 regulates vertebral specification in differentiating somites. Dev Biol. 2012 Sep 15;369(2):308-18