Denis Duboule
Éditions Fayard


Journal Articles

Commentary on paper by Leroy C. Stevens (1960)

D. Duboule 

Developmental Biology. 2019-10-01. Vol. 454, num. 1, p. 1-14. DOI : 10.1016/j.ydbio.2019.07.016.

Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes

E. Rodriguez-Carballo; L. Lopez-Delisle; N. Yakushiji-Kaminatsui; A. Ullate-Agote; D. Duboule 

BMC Biology. 2019-07-12. Vol. 17, p. 55. DOI : 10.1186/s12915-019-0677-x.

Constrained Transcriptional Polarity In The Organization Of Mammalian Hox Gene Clusters

F. Darbellay; C. Bochaton; L. Lopez-Delisle; B. Mascrez; P. Tschopp et al. 

2019-03-14. DOI : 10.1101/572875.

Tail Bud Progenitor Activity Relies on a Network Comprising Gdf11, Lin28, and Hox13 Genes

R. Aires; L. de Lemos; A. Novoa; A. D. Jurberg; B. Mascrez et al. 

Developmental Cell. 2019-02-11. Vol. 48, num. 3, p. 383-+. DOI : 10.1016/j.devcel.2018.12.004.


Analysis of long-range gene regulation at the HoxD locus

A. R. De Carvalho Amândio Lhopitallier / D. Duboule (Dir.)  

Lausanne, EPFL, 2019. 


Journal Articles

Do RET somatic mutations play a role in Hirschsprung disease? Response

B. K. Kragesteen; D. Duboule; S. Mundlos; M. Spielmann 

Genetics In Medicine. 2018-11-01. Vol. 20, num. 11, p. 1481-1482. DOI : 10.1038/gim.2018.20.

Similarities and differences in the regulation of HoxD genes during chick and mouse limb development

N. Yakushiji-Kaminatsui; L. Lopez-Delisle; C. C. Bolt; G. Andrey; L. Beccari et al. 

Plos Biology. 2018-11-01. Vol. 16, num. 11, p. e3000004. DOI : 10.1371/journal.pbio.3000004.

Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

L. Beccari; N. Moris; M. Girgin; D. A. Turner; P. Baillie-Johnson et al. 

Nature. 2018-10-11. Vol. 562, num. 7726, p. 272-+. DOI : 10.1038/s41586-018-0578-0.


Coordinated Hoxd genes expression during embryogenesis is dependent on a strict disposition of genes and polarized regulators within the HoxD cluster

F. Darbellay / D. Duboule (Dir.)  

Lausanne, EPFL, 2018. 


Journal Articles

The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes.

E. Rodriguez-Carballo; L. Lopez-Delisle; Y. Zhan; P. J. Fabre; L. Beccari et al. 

Genes & Development. 2017. Vol. 31, num. 22, p. 2264-2281. DOI : 10.1101/gad.307769.117.

Control of growth and gut maturation by &ITHoxD&IT genes and the associated lncRNA &ITHaglr&IT

J. Zakany; F. Darbellay; B. Mascrez; A. Necsulea; D. Duboule 

Proceedings of the National Academy of Sciences of the United States of America. 2017. Vol. 114, num. 44, p. E9290-E9299. DOI : 10.1073/pnas.1712511114.

Large scale genomic reorganization of topological domains at the HoxD locus

P. J. Fabre; M. Leleu; B. H. Mormann; L. Lopez-Delisle; D. Noordermeer et al. 

Genome Biology. 2017. Vol. 18, num. 1. DOI : 10.1186/s13059-017-1278-z.

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

A. R. Rodrigues; N. Yakushiji-Kaminatsui; Y. Atsuta; G. Andrey; P. Schorderet et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2017. Vol. 114, num. 12, p. 3139-3144. DOI : 10.1073/pnas.1620767114.

Conference Papers

Hox Genes Regulation During Vertebrate Development and Evolution

F. Darbellay; J. Zakany; B. Mascrez; D. Duboule 

2017. 18th International Congress of Developmental Biology, Natil Univ Singapore, Singapore, SINGAPORE, JUN 18-22, 2017. p. S13-S14. DOI : 10.1016/j.mod.2017.04.562.


Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock

J. Deschamps; D. Duboule 

Genes & Development. 2017. Vol. 31, num. 14, p. 1406-1416. DOI : 10.1101/gad.303123.117.


KRAB’n’KAP, DNA methylation and epigenetic memory

A. Coluccio / D. Trono; P. Turelli (Dir.)  

Lausanne, EPFL, 2017. 


Journal Articles

Hotair Is Dispensible for Mouse Development

A. R. Amandio; A. Necsulea; E. Joye; B. Mascrez; D. Duboule 

Plos Genetics. 2016. Vol. 12, num. 12, p. e1006232. DOI : 10.1371/journal.pgen.1006232.

Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

R. Schep; A. Necsulea; E. Rodriguez-Carballo; I. Guerreiro; G. Andrey et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2016. Vol. 113, num. 48, p. E7720-E7729. DOI : 10.1073/pnas.1617141113.

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

I. Guerreiro; S. Gitto; A. Novoa; J. Codourey; H. Thi Hanh Nguyen et al. 

Elife. 2016. Vol. 5, p. e16087. DOI : 10.7554/eLife.16087.

A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus

L. Beccari; N. Yakushiji-Kaminatsui; J. M. Woltering; A. Necsulea; N. Lonfat et al. 

Genes & Development. 2016. Vol. 30, num. 10, p. 1172-1186. DOI : 10.1101/gad.281055.116.

Conference Papers

Nanoscale Spatial Organization of Chromatin in its Cellular Context, from Telomeres to Hox

S. Manley; K. Douglass; V. Pfeiffer; A. Vancevska; P. Fabre et al. 

2016. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, FEB 27-MAR 02, 2016. p. 485A-485A.

A genetic approach of long-range gene regulation during development and evolution

D. Duboule 

2016.  p. 219-220.


From the early steps of whisker formation to its evolutionary disappearance: the (curious) case of Prdm1 and its regulation

P. G. Manti / Y. Barrandon (Dir.)  

Lausanne, EPFL, 2016. 

Book Chapters

Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci

F. Darbellay; D. Duboule 

Essays On Developmental Biology, Pt A; San Diego: Elsevier Academic Press Inc, 2016. p. 299-314.


Journal Articles

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

P. J. Fabre; A. Benke; E. Joye; T. H. Nguyen Huynh; S. Manley et al. 

Proceedings of the National Academy of Sciences of the United States of America. 2015. Vol. 112, num. 45, p. 13964-13969. DOI : 10.1073/pnas.1517972112.

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model

J. M. Woltering; D. Duboule 

Mechanisms Of Development. 2015. Vol. 138, p. 64-72. DOI : 10.1016/j.mod.2015.07.006.

Structure, function and evolution of topologically associating domains (TADs) at HOX loci

N. Lonfat; D. Duboule 

FEBS letters. 2015. Vol. 589, num. 20 Pt A, p. 2869-2876. DOI : 10.1016/j.febslet.2015.04.024.

Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain

M. Vieux-Rochas; P. J. Fabre; M. Leleu; D. Duboule; D. Noordermeer 

Proceedings of the National Academy of Sciences of the United States of America. 2015. Vol. 112, num. 15, p. 4672-7. DOI : 10.1073/pnas.1504783112.


Visualizing the HoxD Gene Cluster at the Nanoscale Level

P. J. Fabre; A. Benke; S. Manley; D. Duboule 

Cold Spring Harbor symposia on quantitative biology. 2015. Vol. 80, p. 9-16. DOI : 10.1101/sqb.2015.80.027177.


Journal Articles

Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci

N. Lonfat; T. Montavon; F. Darbellay; S. Gitto; D. Duboule 

Science. 2014. Vol. 346, num. 6212, p. 1004-1006. DOI : 10.1126/science.1257493.

Considerations when investigating IncRNA function in vivo

A. R. Bassett; A. Akhtar; D. P. Barlow; A. P. Bird; N. Brockdorff et al. 

Elife. 2014. Vol. 3, p. e03058. DOI : 10.7554/eLife.03058.

Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs

J. Lopez-Rios; A. Duchesne; D. Speziale; G. Andrey; K. A. Peterson et al. 

NATURE. 2014. Vol. 511, num. 7507, p. 46-U553. DOI : 10.1038/nature13289.

Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

D. Noordermeer; M. Leleu; P. Schorderet; E. Joye; F. Chabaud et al. 

eLife. 2014. Vol. 3, p. e02557. DOI : 10.7554/eLife.02557.

Evolving Hox Activity Profiles Govern Diversity in Locomotor Systems

H. Jung; E. Mazzoni; N. Soshnikova; O. Hanley; B. Venkatesh et al. 

Developmental Cell. 2014. Vol. 29, num. 2, p. 171-187. DOI : 10.1016/j.devcel.2014.03.008.

SnapShot: Hox Gene Regulation

G. Andrey; D. Duboule 

Cell. 2014. Vol. 156, num. 4. DOI : 10.1016/j.cell.2014.01.060.

Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits

J. M. Woltering; D. Noordermeer; M. Leleu; D. Duboule 

PLoS Biology. 2014. Vol. 12, num. 1, p. e1001773. DOI : 10.1371/journal.pbio.1001773.


Journal Articles

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

F. J. Vonk; N. R. Casewell; C. V. Henkel; A. M. Heimberg; H. J. Jansen et al. 

Proceedings of the National Academy of Sciences. 2013. Vol. 110, num. 51, p. 20651-20656. DOI : 10.1073/pnas.1314702110.

A Genetic Approach to the Recruitment of PRC2 at the HoxD Locus

P. Schorderet; N. Lonfat; F. Darbellay; P. Tschopp; S. Gitto et al. 

PLoS Genetics. 2013. Vol. 9, num. 11, p. e1003951. DOI : 10.1371/journal.pgen.1003951.

Topology of mammalian developmental enhancers and their regulatory landscapes

W. De Laat; D. Duboule 

Nature. 2013. Vol. 502, num. 7472, p. 499-506. DOI : 10.1038/nature12753.

Multiple Enhancers Regulate Hoxd Genes and the Hotdog LncRNA during Cecum Budding

S. Delpretti; T. Montavon; M. Leleu; E. Joye; A. Tzika et al. 

Cell reports. 2013. Vol. 5, num. 1, p. 137-150. DOI : 10.1016/j.celrep.2013.09.002.

Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine

I. Guerreiro; A. Nunes; J. M. Woltering; A. Casaca; A. Novoa et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2013. Vol. 110, num. 26, p. 10682-10686. DOI : 10.1073/pnas.1300592110.

Combined function of HoxA and HoxB clusters in neural crest cells

M. Vieux-Rochas; B. Mascrez; R. Krumlauf; D. Duboule 

Developmental biology. 2013. Vol. 382, num. 1, p. 293-301. DOI : 10.1016/j.ydbio.2013.06.027.

A switch between topological domains underlies HoxD genes collinearity in mouse limbs

G. Andrey; T. Montavon; B. Mascrez; F. Gonzalez; D. Noordermeer et al. 

Science (New York, N.Y.). 2013. Vol. 340, num. 6137, p. 1234167. DOI : 10.1126/science.1234167.

Chromatin architectures and hox gene collinearity

D. Noordermeer; D. Duboule 

Current topics in developmental biology. 2013. Vol. 104, p. 113-48. DOI : 10.1016/B978-0-12-416027-9.00004-8.

Duplications of hox gene clusters and the emergence of vertebrates

N. Soshnikova; R. Dewaele; P. Janvier; R. Krumlauf; D. Duboule 

Developmental biology. 2013. Vol. 378, num. 2, p. 194-199. DOI : 10.1016/j.ydbio.2013.03.004.


Chromatin looping and organization at developmentally regulated gene loci

D. Noordermeer; D. Duboule 

Wiley Interdisciplinary Reviews: Developmental Biology. 2013. Vol. 2, num. 5, p. 615-630. DOI : 10.1002/wdev.103.


An ancestral regulatory mechanism underlies Hoxd gene expression in both developing genitals and digits

N. Lonfat / D. Duboule (Dir.)  

Lausanne, EPFL, 2013. 

Regulatory Switches Underlie Hoxd Gene Activation in Tetrapod Limbs

G. Andrey / D. Duboule (Dir.)  

Lausanne, EPFL, 2013. 

Polycomb Recruitment and Targeting in Mammals

P. Schorderet / D. Duboule (Dir.)  

Lausanne, EPFL, 2013. 

Mechanisms of Hoxd gene regulation during the development and evolution of the intestinal caecum

S. Delpretti Anex / D. Duboule (Dir.)  

Lausanne, EPFL, 2013. 


Journal Articles

A Genetic Basis for Altered Sexual Behavior in Mutant Female Mice

J. Zakany; D. Duboule 

Current Biology. 2012. Vol. 22, num. 18, p. 1676-1680. DOI : 10.1016/j.cub.2012.06.067.

Landscapes and archipelagos: spatial organization of gene regulation in vertebrates

T. Montavon; D. Duboule 

Trends in Cell Biology. 2012. Vol. 22, num. 12, p. 347-354. DOI : 10.1016/j.tcb.2012.04.003.

A function for all posterior Hoxd genes during digit development?

S. Delpretti; J. Zakany; D. Duboule 

Developmental dynamics : an official publication of the American Association of Anatomists. 2012. Vol. 241, num. 4, p. 792-802. DOI : 10.1002/dvdy.23756.

Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters

P. Tschopp; A. J. Christen; D. Duboule 

Development. 2012. Vol. 139, p. 929-939. DOI : 10.1242/dev.076794.


Journal Articles

A regulatory archipelago controls hox genes transcription in digits

T. Montavon; N. Soshnikova; B. Mascrez; E. Joye; L. Thevenet et al. 

Cell. 2011. Vol. 147, num. 5, p. 1132-45. DOI : 10.1016/j.cell.2011.10.023.

A genetic approach to the transcriptional regulation of hox gene clusters

P. Tschopp; D. Duboule 

Annual review of genetics. 2011. Vol. 45, p. 145-66. DOI : 10.1146/annurev-genet-102209-163429.

The dynamic architecture of Hox gene clusters

D. Noordermeer; M. Leleu; E. Splinter; J. Rougemont; W. De Laat et al. 

Science (New York, N.Y.). 2011. Vol. 334, num. 6053, p. 222-5. DOI : 10.1126/science.1207194.

Analysis of the dynamics of limb transcriptomes during mouse development

I. Gyurján; B. Sonderegger; F. Naef; D. Duboule 

BMC developmental biology. 2011. Vol. 11, p. 47. DOI : 10.1186/1471-213X-11-47.

Structural and functional differences in the long non-coding RNA hotair in mouse and human

P. Schorderet; D. Duboule 

PLoS genetics. 2011. Vol. 7, num. 5, p. e1002071. DOI : 10.1371/journal.pgen.1002071.

Reshuffling genomic landscapes to study the regulatory evolution of Hox gene clusters

P. Tschopp; N. Fraudeau; F. Béna; D. Duboule 

Proceedings of the National Academy of Sciences of the United States of America. 2011. Vol. 108, num. 26, p. 10632-10637. DOI : 10.1073/pnas.1102985108.

A regulatory ‘landscape effect’ over the Hoxd cluster

P. Tschopp; D. Duboule 

Developmental Biology. 2011. Vol. 351, p. 288-296. DOI : 10.1016/j.ydbio.2010.12.034.

Conference Papers

Lentiviral vectors mediated transgenesis

S. Verp; M. Blom; M. Friedli; S. Delpretti; I. Barde et al. 

2011.  p. 1170-1170.


Journal Articles

A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the olig1 and olig2 locus

M. Friedli; I. Barde; M. Arcangeli; S. Verp; A. Quazzola et al. 

PloS One. 2010. Vol. 5, num. 12, p. e15741. DOI : 10.1371/journal.pone.0015741.

Functional analysis of CTCF during mammalian limb development

N. Soshnikova; T. Montavon; M. Leleu; N. Galjart; D. Duboule 

Developmental cell. 2010. Vol. 19, num. 6, p. 819-30. DOI : 10.1016/j.devcel.2010.11.009.

Changes in Hox genes’ structure and function during the evolution of the squamate body plan

N. Di-Poï; J. I. Montoya-Burgos; H. Miller; O. Pourquié; M. C. Milinkovitch et al. 

Nature. 2010. Vol. 464, num. 7285, p. 99-103. DOI : 10.1038/nature08789.

Additive and global functions of HoxA cluster genes in mesoderm derivatives

N. Di-Poï; U. Koch; F. Radtke; D. Duboule 

Developmental biology. 2010. Vol. 341, num. 2, p. 488-98. DOI : 10.1016/j.ydbio.2010.03.006.

The origin of digits: expression patterns versus regulatory mechanisms

J. M. Woltering; D. Duboule 

Developmental cell. 2010. Vol. 18, num. 4, p. 526-32. DOI : 10.1016/j.devcel.2010.04.002.

Homeobox genes d11-d13 and a13 control mouse autopod cortical bone and joint formation

P. Villavicencio-Lorini; P. Kuss; J. Friedrich; J. Haupt; M. Farooq et al. 

The Journal of clinical investigation. 2010. Vol. 120, num. 6, p. 1994-2004. DOI : 10.1172/JCI41554.

The evo-devo comet

D. Duboule 

Embo Reports. 2010. Vol. 11, p. 489-489. DOI : 10.1038/embor.2010.94.


Journal Articles

The Hox complex – an interview with Denis Duboule. Interviewed by Richardson, Michael K

D. Duboule 

Int J Dev Biol. 2009. Vol. 53, num. 5-6, p. 717-23. DOI : 10.1387/ijdb.072558mr.

Epigenetic temporal control of mouse Hox genes in vivo

N. Soshnikova; D. Duboule 

Science. 2009. Vol. 324, num. 5932, p. 1320-3. DOI : 10.1126/science.1171468.


Journal Articles

Epigenetic regulation of Hox gene activation: the waltz of methyls

N. Soshnikova; D. Duboule 

Bioessays. 2008. Vol. 30, num. 3, p. 199-202. DOI : 10.1002/bies.20724.

Ectopic nuclear reorganisation driven by a Hoxb1 transgene transposed into Hoxd

C. Morey; N. R. Da Silva; M. Kmita; D. Duboule; W. A. Bickmore 

Journal of lipid research. 2008. Vol. 121, num. 5, p. 571-7. DOI : 10.1242/jcs.023234.

Characterization of mouse Dactylaplasia mutations: a model for human ectrodactyly SHFM3

M. Friedli; S. Nikolaev; R. Lyle; M. Arcangeli; D. Duboule et al. 

Mamm Genome. 2008. Vol. 19, num. 4, p. 272-8. DOI : 10.1007/s00335-008-9106-0.

Genotypic features of lentivirus transgenic mice

M-O. Sauvain; A. P. Dorr; B. Stevenson; A. Quazzola; F. Naef et al. 

Journal of virology. 2008. Vol. 82, num. 14, p. 7111-9. DOI : 10.1128/JVI.00623-08.

Book Chapters

Global Control Regions and Regulatory Landscapes in Vertebrate Development and Evolution

F. Spitz; D. Duboule 

Long-Range Control of Gene Expression; Elsevier Inc, 2008. p. 175-205.

Student Projects

Direct Reprogramming of Terminally Differentiated Mature B Lymphocytes to Pluripotency

P. Schorderet 


Hoxd gene regulation in the developing caecum

S. Delpretti; T. Montavon 




The rise and fall of Hox gene clusters

D. Duboule 

Development. 2007. Vol. 134, num. 14, p. 2549-60.


Journal Articles

The European dimension for the mouse genome mutagenesis program

J. Auwerx; P. Avner; R. Baldock; A. Ballabio; R. Balling et al. 

Nature genetics. 2004. Vol. 36, num. 9, p. 925-7. DOI : 10.1038/ng0904-925.