Gene Expression Literature Summary

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

Hoxd13  homeobox D13   (Synonyms: Hox-4.8, spdh)
Results	Reference
1	J:220960 Akiyama R, Kawakami H, Wong J, Oishi I, Nishinakamura R, Kawakami Y, Sall4-Gli3 system in early limb progenitors is essential for the development of limb skeletal elements. Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):5075-80
1*	J:75699 Albrecht AN, Schwabe GC, Stricker S, Boddrich A, Wanker EE, Mundlos S, The synpolydactyly homolog (spdh) mutation in the mouse -- a defect in patterning and growth of limb cartilage elements. Mech Dev. 2002 Mar;112(1-2):53-67
1	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: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:309510 Beccari L, Jaquier G, Lopez-Delisle L, Rodriguez-Carballo E, Mascrez B, Gitto S, Woltering J, Duboule D, Dbx2 regulation in limbs suggests interTAD sharing of enhancers. Dev Dyn. 2021 Sep;250(9):1280-1299
1	J:231885 Beccari L, Yakushiji-Kaminatsui N, Woltering JM, Necsulea A, Lonfat N, Rodriguez-Carballo E, Mascrez B, Yamamoto S, Kuroiwa A, Duboule D, A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus. Genes Dev. 2016 May 15;30(10):1172-86
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
1	J:232486 Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N, Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. PLoS Genet. 2016 Mar;12(3):e1005738
1*	J:78766 Boulet AM, Capecchi MR, Duplication of the Hoxd11 gene causes alterations in the axial and appendicular skeleton of the mouse. Dev Biol. 2002 Sep 1;249(1):96-107
1*	J:71694 Bruneau S, Johnson KR, Yamamoto M, Kuroiwa A, Duboule D, The mouse hoxd13(spdh) mutation, a polyalanine expansion similar to human type ii synpolydactyly (spd), disrupts the function but not the expression of other hoxd genes. Dev Biol. 2001 Sep 15;237(2):345-53
1	J:48000 Brunet LJ, McMahon JA, McMahon AP, Harland RM, Noggin, cartilage morphogenesis, and joint formation in the mammalian skeleton [see comments]. Science. 1998 May 29;280(5368):1455-7
1*	J:39658 Buscher D, Bosse B, Heymer J, Ruther U, Evidence for genetic control of Sonic hedgehog by Gli3 in mouse limb development. Mech Dev. 1997 Mar;62(2):175-82
1*	J:274320 Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J, The single-cell transcriptional landscape of mammalian organogenesis. Nature. 2019 Feb;566(7745):496-502
1*	J:71186 Chiang C, Litingtung Y, Harris MP, Simandl BK, Li Y, Beachy PA, Fallon JF, Manifestation of the limb prepattern: limb development in the absence of sonic hedgehog function. Dev Biol. 2001 Aug 15;236(2):421-35
1*	J:98919 Cobb J, Duboule D, Comparative analysis of genes downstream of the Hoxd cluster in developing digits and external genitalia. Development. 2005 Jul;132(13):3055-67
1*	J:153164 Cocquempot O, Brault V, Babinet C, Herault Y, Fork stalling and template switching as a mechanism for polyalanine tract expansion affecting the DYC mutant of HOXD13, a new murine model of synpolydactyly. Genetics. 2009 Sep;183(1):23-30
1	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
1*	J:181619 Delpretti S, Zakany J, Duboule D, A function for all posterior Hoxd genes during digit development?. Dev Dyn. 2012 Apr;241(4):792-802
1*	J:15507 Dolle P, Dierich A, LeMeur M, Schimmang T, Schuhbaur B, Chambon P, Duboule D, Disruption of the Hoxd-13 gene induces localized heterochrony leading to mice with neotenic limbs. Cell. 1993 Nov 5;75(3):431-41
1*	J:54066 Dupe V, Ghyselinck NB, Thomazy V, Nagy L, Davies PJA, Chambon P, Mark M, Essential roles of retinoic acid signaling in interdigital apoptosis and control of BMP-7 expression in mouse autopods. Dev Biol. 1999 Apr 1;208(1):30-43
1*	J:172775 Gildea DE, Luetkemeier ES, Bao X, Loftus SK, Mackem S, Yang Y, Pavan WJ, Biesecker LG, The pleiotropic mouse phenotype extra-toes spotting is caused by translation initiation factor Eif3c mutations and is associated with disrupted sonic hedgehog signaling. FASEB J. 2011 May;25(5):1596-605
1	J:48055 Hecksher-Sorensen J, Hill RE, Lettice L, Double labeling for whole-mount in situ hybridization in mouse. Biotechniques. 1998 Jun;24(6):914-6, 918
1*	J:149502 Hill P, Gotz K, Ruther U, A SHH-independent regulation of Gli3 is a significant determinant of anteroposterior patterning of the limb bud. Dev Biol. 2009 Apr 15;328(2):506-16
1	J:125087 Hill P, Wang B, Ruther U, The molecular basis of Pallister Hall associated polydactyly. Hum Mol Genet. 2007 Sep 1;16(17):2089-96
1	J:242611 Huang BL, Trofka A, Furusawa A, Norrie JL, Rabinowitz AH, Vokes SA, Mark Taketo M, Zakany J, Mackem S, An interdigit signalling centre instructs coordinate phalanx-joint formation governed by 5'Hoxd-Gli3 antagonism. Nat Commun. 2016 Oct 07;7:12903
1*	J:66531 Kraus P, Fraidenraich D, Loomis CA, Some distal limb structures develop in mice lacking Sonic hedgehog signaling. Mech Dev. 2001 Jan;100(1):45-58
1	J:102949 Li C, Xu X, Nelson DK, Williams T, Kuehn MR, Deng CX, FGFR1 function at the earliest stages of mouse limb development plays an indispensable role in subsequent autopod morphogenesis. Development. 2005 Nov;132(21):4755-64
1	J:235489 Li J, Wang Q, Cui Y, Yang X, Li Y, Zhang X, Qiu M, Zhang Z, Zhang Z, Suppressor of Fused Is Required for Determining Digit Number and Identity via Gli3/Fgfs/Gremlin. PLoS One. 2015;10(5):e0128006
1	J:223057 Lin C, Yin Y, Bell SM, Veith GM, Chen H, Huh SH, Ornitz DM, Ma L, Delineating a conserved genetic cassette promoting outgrowth of body appendages. PLoS Genet. 2013;9(1):e1003231
1	J:78941 Litingtung Y, Dahn RD, Li Y, Fallon JF, Chiang C, Shh and Gli3 are dispensable for limb skeleton formation but regulate digit number and identity. Nature. 2002 Aug 29;418(6901):979-83
1	J:79482 Liu Y, Liu C, Yamada Y, Fan CM, growth arrest specific gene 1 acts as a region-specific mediator of the Fgf10/Fgf8 regulatory loop in the limb. Development. 2002 Nov;129(22):5289-300
1	J:184012 Lopez-Rios J, Speziale D, Robay D, Scotti M, Osterwalder M, Nusspaumer G, Galli A, Hollander GA, Kmita M, Zeller R, GLI3 constrains digit number by controlling both progenitor proliferation and BMP-dependent exit to chondrogenesis. Dev Cell. 2012 Apr 17;22(4):837-48
1	J:136057 Lu P, Yu Y, Perdue Y, Werb Z, The apical ectodermal ridge is a timer for generating distal limb progenitors. Development. 2008 Apr;135(8):1395-405
1	J:334725 Markman S, Zada M, David E, Giladi A, Amit I, Zelzer E, A single-cell census of mouse limb development identifies complex spatiotemporal dynamics of skeleton formation. Dev Cell. 2023 Apr 10;58(7):565-581.e4
1	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:178930 Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, Splinter E, de Laat W, Spitz F, Duboule D, A regulatory archipelago controls hox genes transcription in digits. Cell. 2011 Nov 23;147(5):1132-45
1	J:192248 Montavon T, Thevenet L, Duboule D, Impact of copy number variations (CNVs) on long-range gene regulation at the HoxD locus. Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20204-11
1	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:199568 Neufeld SJ, Zhou X, Vize PD, Cobb J, mRNA fluorescence in situ hybridization to determine overlapping gene expression in whole-mount mouse embryos. Dev Dyn. 2013 Sep;242(9):1094-100
1	J:237505 Norrie JL, Li Q, Co S, Huang BL, Ding D, Uy JC, Ji Z, Mackem S, Bedford MT, Galli A, Ji H, Vokes SA, PRMT5 is essential for the maintenance of chondrogenic progenitor cells in the limb bud. Development. 2016 Dec 15;143(24):4608-4619
1*	J:77812 Perriton CL, Powles N, Chiang C, Maconochie MK, Cohn MJ, Sonic hedgehog signaling from the urethral epithelium controls external genital development. Dev Biol. 2002 Jul 1;247(1):26-46
1*	J:56986 Post LC, Innis JW, Altered Hox expression and increased cell death distinguish Hypodactyly from Hoxa13 null mice. Int J Dev Biol. 1999 Jul;43(4):287-94
1	J:134490 Raz R, Stricker S, Gazzerro E, Clor JL, Witte F, Nistala H, Zabski S, Pereira RC, Stadmeyer L, Wang X, Gowen L, Sleeman MW, Yancopoulos GD, Canalis E, Mundlos S, Valenzuela DM, Economides AN, The mutation ROR2W749X, linked to human BDB, is a recessive mutation in the mouse, causing brachydactyly, mediating patterning of joints and modeling recessive Robinow syndrome. Development. 2008 May;135(9):1713-23
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:260451 Rodriguez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D, The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev. 2017 Nov 15;31(22):2264-2281
1	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
1*	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:192010 Sheth R, Marcon L, Bastida MF, Junco M, Quintana L, Dahn R, Kmita M, Sharpe J, Ros MA, Hox genes regulate digit patterning by controlling the wavelength of a Turing-type mechanism. Science. 2012 Dec 14;338(6113):1476-80
1	J:137353 Sohaskey ML, Yu J, Diaz MA, Plaas AH, Harland RM, JAWS coordinates chondrogenesis and synovial joint positioning. Development. 2008 Jul;135(13):2215-20
1	J:83372 Spitz F, Gonzalez F, Duboule D, A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell. 2003 May 2;113(3):405-17
1	J:154460 Suzuki D, Yamada A, Amano T, Yasuhara R, Kimura A, Sakahara M, Tsumaki N, Takeda S, Tamura M, Nakamura M, Wada N, Nohno T, Shiroishi T, Aiba A, Kamijo R, Essential mesenchymal role of small GTPase Rac1 in interdigital programmed cell death during limb development. Dev Biol. 2009 Nov 15;335(2):396-406
1*	J:45575 Takagi T, Moribe H, Kondoh H, Higashi Y, DeltaEF1, a zinc finger and homeodomain transcription factor, is required for skeleton patterning in multiple lineages. Development. 1998 Jan;125(1):21-31
1	J:101736 Verheyden JM, Lewandoski M, Deng C, Harfe BD, Sun X, Conditional inactivation of Fgfr1 in mouse defines its role in limb bud establishment, outgrowth and digit patterning. Development. 2005 Oct;132(19):4235-45
1*	J:96550 Williams TM, Williams ME, Kuick R, Misek D, McDonagh K, Hanash S, Innis JW, Candidate downstream regulated genes of HOX group 13 transcription factors with and without monomeric DNA binding capability. Dev Biol. 2005 Mar 15;279(2):462-80
1	J:175770 Wyngaarden LA, Delgado-Olguin P, Su IH, Bruneau BG, Hopyan S, Ezh2 regulates anteroposterior axis specification and proximodistal axis elongation in the developing limb. Development. 2011 Sep;138(17):3759-67
1	J:56002 Xu X, Weinstein M, Li C, Deng C, Fibroblast growth factor receptors (FGFRs) and their roles in limb development. Cell Tissue Res. 1999 Apr;296(1):33-43
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
1	J:154781 Young T, Rowland JE, van de Ven C, Bialecka M, Novoa A, Carapuco M, van Nes J, de Graaff W, Duluc I, Freund JN, Beck F, Mallo M, Deschamps J, Cdx and Hox genes differentially regulate posterior axial growth in mammalian embryos. Dev Cell. 2009 Oct;17(4):516-26
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:61723 Zhang Z, Yu X, Zhang Y, Geronimo B, Lovlie A, Fromm SH, Chen Y, Targeted misexpression of constitutively active BMP receptor-IB causes bifurcation, duplication, and posterior transformation of digit in mouse limb. Dev Biol. 2000 Apr 15;220(2):154-67
1	J:184918 Zhu X, Zhu H, Zhang L, Huang S, Cao J, Ma G, Feng G, He L, Yang Y, Guo X, Wls-mediated Wnts differentially regulate distal limb patterning and tissue morphogenesis. Dev Biol. 2012 May 15;365(2):328-38