Filippo M. Rijli

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Jun 6, 2023
Building face structures by remote control
Aug 8, 2022
Filippo Rijli elected to Accademia Nazionale dei Lincei
Oct 21, 2021
Meet Dania Machlab, Doktorandin in Bioinformatik
Feb 18, 2021
New-found molecular signature keeps key genes ready for action
Jun 22, 2020
Building corticocerebellar neural circuits
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Filippo M. Rijli

Transcriptional and epigenetic regulation of craniofacial and neuronal development

Our recent work focuses on the transcriptional and epigenetic mechanisms underlying craniofacial development and the sensory mapping of facial structures in the brain. To this end, we established in vivo genome-wide approaches to identify chromatin signatures underlying the molecular identities of selected subpopulations of cranial neural crest cells and neurons of the somatosensory circuits in the mouse hindbrain (brainstem). Moreover, to explore the transcriptional mechanisms of assembly of sensory connectivity maps, we study the functional role of the Hox gene family encoding homeodomain transcription factors. We also address the role of selected epigenetic regulators, including members of Polycomb repressive complexes.

The ad hoc genetic tools we use in mice include imaging of fluorescently labeled neurons and axonal tracts, trans-synaptic viral tracing of defined subpopulations, in utero electroporation, and in vivo genome-wide analysis of gene expression and chromatin organization of cell subpopulations.

Our studies may enhance understanding of the basic molecular mechanisms that establish precise connectivity between neurons and contribute to the definition of the etiology of certain developmental craniofacial syndromes.

Filippo M. Rijli

This is a list of selected publications from this group. For a full list of publications, please visit our Publications page and search by group name.

Kessler S, Minoux M, Joshi O, Ben Zouari Y, Ducret S, Ross F, Vilain N, Salvi A, Wolff J, Kohler H, Stadler MB, Rijli FM (2023) A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest

Nat Commun. 2023 Jun 5;14(1):3242

Selleri L, Rijli FM (2023) Shaping faces: genetic and epigenetic control of craniofacial morphogenesis

Nat Rev Genet. 2023 Apr 24

Pumo GM, Kitazawa T, Rijli FM (2022) Epigenetic and Transcriptional Regulation of Spontaneous and Sensory Activity Dependent Programs During Neuronal Circuit Development

Front Neural Circuits. 2022 May 18;16:911023

Genescu I, Anibal-Martinez M, Kouskoff V, Chenouard N, Mailhes-Hamon C, Cartonnet H, Lokmane L, Rijli FM, López-Bendito G, Gambino F, Garel S (2022) Dynamic interplay between thalamic activity and Cajal-Retzius cells regulates the wiring of cortical layer 1

Cell Rep. 2022 Apr 12;39(2):110667

Kitazawa T, Minoux M, Ducret S, Rijli FM (2022) Different Ectopic Hoxa2 Expression Levels in Mouse Cranial Neural Crest Cells Result in Distinct Craniofacial Anomalies and Homeotic Phenotypes

J Dev Biol. 2022 Jan 31;10(1):9

Machlab D, Burger L, Soneson C, Rijli FM, Schübeler D, Stadler MB (2022) monaLisa: an R/Bioconductor package for identifying regulatory motifs

Bioinformatics. 2022 Apr 28;38(9):2624-2625

Taro Kitazawa, Dania Machlab, Onkar Joshi, Nicola Maiorano, Hubertus Kohler, Sebastien Ducret, Sandra Kessler, Henrik Gezelius, Charlotte Soneson, Panagiotis Papasaikas, Guillermina Lopez-Bendito, Michael B. Stadler and Filippo M. Rijli (2021) A unique bipartite Polycomb signature regulates stimulus-response transcription during development

Nat Genet. 2021 Mar;53(3):379-391

Maheshwari U, Kraus D, Vilain N, Holwerda SJB, Cankovic V, Maiorano NA, Kohler H, Satoh D, Sigrist M, Arber S, Kratochwil CF, Di Meglio T, Ducret S, Rijli FM (2020) Postmitotic Hoxa5 Expression Specifies Pontine Neuron Positional Identity and Input Connectivity of Cortical Afferent Subsets.

Cell Rep. 2020 Jun 16;31(11):107767

Riva M, Genescu I, Habermacher C, Orduz D, Ledonne F, Rijli FM, Lopez-Bendito G, Coppola E, Garel S, Angulo MC, Pierani A. (2019) Activity-dependent death of transient Cajal-Retzius neurons is required for functional cortical wiring.

Elife. 2019 Dec 31;8:e50503

Coughlan E, Garside VC, Wong SFL, Liang H, Kraus D, Karmakar K, Maheshwari U, Rijli FM, Bourne J, McGlinn E. (2019) A Hox Code Defines Spinocerebellar Neuron Subtype Regionalization.

Cell Rep. 2019 Nov 19;29(8):2408-2421.e4

Kitazawa T, Rijli FM (2018) Barrelette map formation in the prenatal mouse brainstem

Curr Opin Neurobiol 53:210-219

Kitazawa T, Rijli FM (2018) Integrating into the Rhombomere Community across the Border

Dev Cell 45(5):546-548

Kitazawa T, Rijli FM (2017) Nuclear pore protein meets transcription factor in neural fate

Neuron 96:259-261

Minoux M, Holwerda S, Vitobello A, Kitazawa T, Kohler H, Stadler M, Rijli FM (2017) Gene bivalency at polycomb domains regulates cranial neural crest positional identity

Science, 355:eaal2913

Karmakar K, Narita Y, Fadok J, Loche A, Fadok J, Genoud C, Ducret S, Di Meglio T, Thierry R, Bacelo J, Lüthi A, Rijli FM (2017) Hoxa2 and Hoxb2 are required for tonotopic map precision and sound discrimination in the mouse auditory brainstem

Cell Reports, 18:185-197

Moreno-Juan V, Filipchuk A, Antón-Bolaños N, Mezzera C, Gezelius H, Andrés B, Rodriguez Malmierca L, Susín R, Schaad O, Rutlin M, Nelson S, Ducret S, Valdeolmillos M, Rijli FM, López-Bendito G (2017) Prenatal thalamic waves regulate cortical area size prior to sensory processing

Nature Comm, 8:14172

Bechara A, Laumonnerie C, Vilain N, Kratochwil CF, Cankovic V, Maiorano NA, Kirschmann MA, Ducret S, Rijli FM (2015) Hoxa2 selects barrelette neuron identity and connectivity in the mouse somatosensory brainstem

Cell Reports. 2015 Oct. [Epub ahead of print]

Laumonnerie C*, Bechara A*, Vilain N, Kurihara Y, Kurihara H, Rijli FM (2015) Facial whisker pattern is not sufficient to instruct a whisker-related topographic map in the mouse somatosensory brainstem.

Development. 2015 Sep. [Epub ahead of print]
* co-first authors

Minoux M, Kratochwil CF, Ducret S, Amin S, Kitazawa T, Kurihara H, Bobola N, Vilain N, Rijli FM (2013) Mouse Hoxa2 mutations provide a model for microtia and auricle duplication

Development 140:4386-97

Di Bonito M, Narita Y, Avallone B, Sequino L, Mancuso M, Andolfi G, Franzè AM, Puelles L, Rijli FM*, Studer M* (2013) Assembly of the auditory circuitry by a hox genetic network in the mouse brainstem

PLoS Genet 9:e1003249
* corresponding authors

Di Meglio T, Kratochwil CF, Vilain N, Loche A, Vitobello A, Yonehara K, Hrycaj SM, Roska B, Peters AHFM, Eichmann A, Wellik D, Ducret S, Rijli FM (2013) Ezh2 orchestrates topographic tangential migration and connectivity of mouse precerebellar neurons

Science, 339:204-207

Vitobello A, Ferretti E, Lampe X, Vilain N, Ducret S, Ori M, Spetz JF, Selleri L, Rijli FM (2011) Hox and Pbx factors control retinoic acid synthesis during hindbrain segmentation

Dev Cell. 20:469-82

Erzurumlu RS, Murakami Y, Rijli FM (2010) Mapping the face in the somatosensory brainstem

Nat Rev Neurosci 11:252-63

Minoux M, Rijli FM (2010) Molecular mechanisms of cranial neural crest cell migration and patterning in craniofacial development

Development 137(16):2605-21

Minoux M, Antonarakis GS, Kmita M, Duboule D, Rijli FM (2009) Rostral and caudal pharyngeal arches share a common neural crest ground pattern

Development 136:637-645

Geisen MJ, Di Meglio T, Pasqualetti M, Ducret S, Brunet JF, Chedotal A, Rijli FM (2008) Hox paralogue group 2 genes control the migration of mouse pontine neurons through slit-robo signaling

PLoS Biol;6(6):e142

Oury F, Murakami Y, Renaud JS, Pasqualetti M, Charnay P, Ren SY, Rijli FM (2006) Hoxa2- and rhombomere-dependent development of the mouse facial somatosensory map

Science 313:1408-1413

Full list of publications
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Group leader

In current position since 2008
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PhD students

In current position since 2021
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In current position since 2021
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In current position since 2019
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Postdoctoral fellows

In current position since 2018
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In current position since 2017
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In current position since 2019
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Technical/Research associates

In current position since 2008
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In current position since 2023
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In current position since 2008
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Visiting scientists

In current position since 2009
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PhD students

Sandra Kessler (2017-2023)
Leslie Bargsted (2016-2022)
Dania Machlab (2016-2021)
Upasana Maheshwari (2014-2020)
Xinyu Liu (2016)
Dominik Kraus (2011-2016)
Alberto Loche (2011-2016)
Kajari Karmakar (2009-2015)
Claudius Kratochwil (2008-2013)
Antonio Vitobello (2008-2013)
Christophe Laumonnerie (2008-2011)

Postdoctoral fellows

Sandra Kessler (2023)
Joachim Wolff (2022)
Taro Kitazawa (2015-2022)
Dania Machlab (2022)
Yannick Hauser (2021)
Huanhuan Li (2018-2021)
Upasana Maheshwari (2020)
Nicola Maiorano (2013-2016)
Vanja Cankovic (2013-2015)
Sjoerd Holwerda (2013-2015)
Ahmad Bechara (2008-2015)
Thomas Di Meglio (2009-2012)
Yuichi Narita (2008-2011)
Liseth Parra (2009-2010)


Cynthia Ehrhard (2020)

Visiting scientists

Mar Anibal Martinez (2018)


PhD, University of Pisa, Italy
MSc, University of Pisa, Italy

Positions held

Senior Group Leader, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
Directeur de Recherche, Centre National de la Recherche Scientifique (CNRS), Paris, France
Group Leader, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC) Strasbourg, France
Chargé de Recherche at Centre National de la Recherche Scientifique (CNRS), Paris, France
Postdoctoral Fellow, Laboratory of Molecular Genetics of Eucaryotes (LGME), Strasbourg, France
Predoctoral Fellow, Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, USA


Elected member of the Accademia Nazionale dei Lincei
ERC Synergy Grant
Titular Professor in Neurobiology, University of Basel
Privatdozent, University of Basel
Prix Lacassagne du Collège de France
Fondation pour la Recherche Medicale Award
Vice-Chair National Committee 3, French Cancer Research Association
Member, Faculty of 1000, Developmental Biology
Editorial Board, Development
Habilitation à Diriger des Recherches (HDR), University Louis Pasteur, Strasbourg, France
EMBO Short-Term Fellowship
EMBO Long-Term Fellowship