Andrey Lab



Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development
Darbellay  F., Ramisch  A., Lopez-Delisle  L., Kosicki  M., Rauseo  A., Jouini  Z., Visel  A., Andrey G.
Nat Commun. 2024 Jun 6;15(1):4820. doi: 10.1038/s41467-024-49203-2.

Temporal constraints on enhancer usage shape the regulation of limb gene transcription
Rouco R., Rauseo A., Sapin G., Bompadre A., Darbellay F., Andrey G.
bioRxiv, 2024.2003.2022.585864 (2024); doi:

Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells
Bompadre O.,
Rouco R., Darbellay F., Rauseo R., Guerard-Millet F., Gentile C., Kmita M. and Andrey G.
bioRxiv, 2024.2003.2004.582675; doi:


Inhibitory SMAD6 interferes with BMP dependent generation of muscle progenitor cells and perturbs. proximodistal pattern of murine limb muscles
Asfour H., Hirsinger E., Rouco R., Zarrouki F., Hayashi S., Swist S., Braun T., Patel K., Relaix F., Andrey G., Stricker S., Duprez D., Stantzou A., Amthor H.
Development. 2023 May 23:dev.201504. doi: 10.1242/dev.201504.

Genetic cold cases; lessons from solving complex congenital limb disorders
Andrey G.
and Duboule D.


News and Views: MAZ regulates chromatin domain insulation and genome architecture
Darbellay F., Rouco R., Andrey  G.

Nat Genet. 2022 Feb;54(2):96-97. doi: 10.1038/s41588-021-00995-9.

Context-Dependent Enhancer Function Revealed by Targeted Inter-TAD Relocation
Bolt C., Lopez-Delisle L., Hintermann A., Mascrez B., Rauseo A., Andrey G., Denis Duboule
Nat Commun 13, 3488 (2022).


Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer
Rouco R., Bompadre O., Rauseo A., Fazio O., Peraldi R., Thorel F. and Andrey G.

Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator
Allou L., Balzano S., Magg. A., Quinodoz M., Royer-Bertrand B., Schöpflin R., Chan WL, Speck-Martins C., Carvalho D., Farage L., Lourenço C., Albuquerque R., Rajagopal S., Nampoothiri S., Campos-Xavier B., Chiesa C., Niel-Bütschi F., Wittler L., Timmermann B,, Spielmann M., Robson M.I., Ringel A., Heinrich V., Cova G., Andrey G., Prada C., Pescini-Gobert R., Unger S., Bonafé L, Grote P, Rivolta C., Mundlos S. and Superti-Furga A.
Nature. 2021 Feb 10.doi: 10.1038/s41586-021-03208-9.


A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival
Abassah-Oppong S, Mannion B., Tissières V., Rodríguez-Carballo E., Ljubojevic A., Fabrice Darbellay, Festa T., Sullivan C., Kelman G., Hunter R., Novak C., Plajzer-Frick I., Tran S., Akiyama J., Barozzi I., Andrey G., Lopez-Rios J., Dickel D., Visel A., Pennacchio L., Cobb J., Osterwalder M.
bioRxiv 2020.11.22.393173; doi:


Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells.
Bianco S., Annunziatella C., Andrey G., Chiariello A.M., Esposito A., Fiorillo L., Prisco A., Conte M., Campanile R., Nicodemi M..
Cell Rep. 2019 Aug 6;28(6):1574-1583.e4. doi: 10.1016/j.celrep.2019.07.013.

Preformed Chromatin Topology Assists Transcriptional Robustness of Shh during Limb Development.
Paliou C., Guckelberger P., Schöpflin R., Heinrich V.Esposito A., Chiariello A.M., Bianco s., Annunziatella C., Helmuth J., Haas S., Jerković I., Brieske N., Wittler L., Timmermann B., Nicodemi M.Vingron M., Mundlos S, Andrey G.
Proc Natl Acad Sci U S A. 2019 May 30. pii: 201900672. doi: 10.1073/pnas.1900672116

Chromatin topology in development and disease.
Bompadre O., Andrey G.
Curr Opin Genet Dev. 2019 May 21;  55: 32-38 doi: 10.1016/j.gde.2019.04.007

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations.
Kraft K., Magg A., Heinrich V., Riemenschneider C., Schöpflin R., Markowski J., Ibrahim D.M., Acuna-Hidalgo R., Despang A., Andrey G., Wittler L., Timmermann B., Vingron M., Mundlos S.
Nat Cell Biol. 2019 Feb 11. doi: 10.1038/s41556-019-0273-x


Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis.
Kragesteen BK, Spielmann M, Paliou C, Heinrich V, Schöpflin R, Esposito A, Annunziatella C, Bianco S, Chiariello AM, Jerković I, Harabula I, Guckelberger P, Pechstein M, Wittler L, Chan WL, Franke M, Lupiáñez DG, Kraft K, Timmermann B, Vingron M, Visel A, Nicodemi M, Mundlos S, Andrey G.
Nat Genet. 2018 Oct;50(10):1463-1473. doi: 10.1038/s41588-018-0221-x. Epub 2018 Sep 27.

Similarities and differences in the regulation of HoxD genes during chick and mouse limb development.
Yakushiji-Kaminatsui N, Lopez-Delisle L, Bolt CB, Andrey G, Beccari L, Duboule.
PLoS Biol. 2018 Nov 26;16(11):e3000004. doi: 10.1371/journal.pbio.3000004. eCollection 2018 Nov.

Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture.
Bianco S, Lupiáñez DG, Chiariello AM, Annunziatella C, Kraft K, Schöpflin R, Wittler L, Andrey G, Vingron M, Pombo A, Mundlos S, Nicodemi M.
Nat Genet. 2018 Apr 16. doi: 10.1038/s41588-018-0098-8.

Large genomic insertion at the Shh locus results in hammer toes through enhancer adoption.
Paliou C, Andrey G.
Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):839-841. doi: 10.1073/pnas.1721351115. Epub 2018 Jan 12.


The three-dimensional genome: regulating gene expression during pluripotency and development.
Andrey G, Mundlos S.
Development. 2017 Oct 15;144(20):3646-3658. doi: 10.1242/dev.148304. Review.

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells.
Rodrigues AR, Yakushiji-Kaminatsui N, Atsuta Y, Andrey G, Schorderet P, Duboule D, Tabin CJ.
Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3139-3144. doi: 10.1073/pnas.1620767114.

Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF.
Jerković I, Ibrahim DM, Andrey G, Haas S, Hansen P, Janetzki C, González Navarrete I, Robinson PN, Hecht J, Mundlos S.
PLoS Genet. 2017 Jan 19;13(1):e1006567. doi: 10.1371/journal.pgen.1006567. eCollection 2017 Jan.

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding.
Andrey G, Schöpflin R, Jerković I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S.
Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6.

CRISPR/Cas9 Genome Editing in Embryonic Stem Cells.
Andrey G, Spielmann M.
Methods Mol Biol. 2017;1468:221-34. doi: 10.1007/978-1-4939-4035-6_15.


Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape.
Schep R, Necsulea A, Rodríguez-Carballo E, Guerreiro I, Andrey G, Nguyen Huynh TH, Marcet V, Zákány J, Duboule D, Beccari L.
Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7720-E7729. Epub 2016 Nov 15.

Formation of new chromatin domains determines pathogenicity of genomic duplications.
Franke M, Ibrahim DM, Andrey G, Schwarzer W, Heinrich V, Schöpflin R, Kraft K, Kempfer R, Jerković I, Chan WL, Spielmann M, Timmermann B, Wittler L, Kurth I, Cambiaso P, Zuffardi O, Houge G, Lambie L, Brancati F, Pombo A, Vingron M, Spitz F, Mundlos S.
Nature. 2016 Oct 13;538(7624):265-269. doi: 10.1038/nature19800. Epub 2016 Oct 5.


Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice.
Kraft K, Geuer S, Will AJ, Chan WL, Paliou C, Borschiwer M, Harabula I, Wittler L, Franke M, Ibrahim DM, Kragesteen BK, Spielmann M, Mundlos S, Lupiáñez DG, Andrey G.
Cell Rep. 2015 Feb 4. pii: S2211-1247(15)00029-7. doi: 10.1016/j.celrep.2015.01.016.


Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs.
Lopez-Rios J, Duchesne A, Speziale D, Andrey G, Peterson KA, Germann P, Unal E, Liu J, Floriot S, Barbey S, Gallard Y, Müller-Gerbl M, Courtney AD, Klopp C, Rodriguez S, Ivanek R, Beisel C, Wicking C, Iber D, Robert B, McMahon AP, Duboule D, Zeller R.
Nature. 2014 Jul 3;511(7507):46-51. doi: 10.1038/nature13289.

SnapShot: Hox gene regulation.
Andrey G, Duboule D.
Cell. 2014 Feb 13;156(4):856-856.e1. doi: 10.1016/j.cell.2014.01.060.


A switch between topological domains underlies HoxD genes collinearity in mouse limbs.
Andrey G, Montavon T, Mascrez B, Gonzalez F, Noordermeer D, Leleu M, Trono D, Spitz F, Duboule D.
Science. 2013 Jun 7;340(6137):1234167. doi: 10.1126/science.1234167.