Gambetta Lab / Center for Integrative Genomics

We aim to understand the molecular basis of gene regulation specificity in Drosophila using genetics, genomics, biochemistry and live-imaging tools.

Research

In multicellular organisms, genes are turned ON and OFF in robust spatial and temporal patterns. Regulatory elements that activate or silence gene transcription are inherently promiscuous and can act over long genomic distances. A basic question is how regulatory elements find their target promoters and restrict their activity to their targets.

On the one hand, we study how regulatory crosstalk is prevented. Insulators were discovered in Drosophila and subsequently in various organisms from yeast to humans, as DNA elements that block communication between a regulatory element and a gene promoter when placed in between. In flies and humans, insulators exert their activity by recruiting insulator proteins. We study the biological relevance and molecular mechanisms of insulator proteins.

On the other hand, we study how genes find their appropriate regulatory elements across surprisingly long genomic distances and skip over non-target genes. We address the biological relevance of these interactions by disrupting them, and we study how they form.

Our studies in flies reveal new evolutionary perspectives into the relevance of 3D genome folding for correctly wiring genes to their regulatory elements.

Gambetta Lab research

Publications

Essential role of Cp190 in physical and regulatory boundary formation

Anjali Kaushal, Julien Dorier, Bihan Wang, Giriram Mohana, Michael Taschner, Pascal Cousin, Patrice Waridel, Christian Iseli, Anastasiia Semenova, Simon Restrepo, Nicolas Guex, Erez Lieberman Aiden & Maria Cristina Gambetta

Science Advances 2022 · DOI / WOSUID

Graphical abstract

essential-role-of-Cp190-abstract
  • Whereas CTCF and other DNA-binding proteins only bind to a subset of fly contact domain boundaries, Cp190 is present at a large fraction of boundaries.
  • Flies use Cp190 as an adaptor protein recruited by DNA-bound proteins such as CTCF and others to form boundaries.
  • DNA-bound CTCF cannot form a robust boundary in the absence of Cp190 (despite CTCF’s conserved ability to directly interact with cohesin).
  • Overall, Cp190 is required to form most promoter-distal boundaries but is dispensable to form promoter-proximal boundaries.
  • Cp190 is thus currently the major player in fly boundary formation.
  • Cp190 assembles into diverse multisubunit complexes that share similar enhancer-blocking activity in a quantitative insulator reporter assay.
  • Cp190 is essential for early development and prevents regulatory cross-talk between specific gene loci that pattern the fly embryo.
  • Cp190 is, in contrast, dispensable for long-range enhancer-promoter communication at tested loci.
  • This work demonstrates that diverse mechanisms evolved to partition genomes into independent physical and regulatory domains.
  • This work also reveals that the enhancer-blocking and enhancer-enabling functions typically ascribed to fly insulators are separable.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

C. Hoencamp, O. Dudchenko, A.M.O. Elbatsh, S. Brahmachari, J.A. Raaijmakers, T. van Schaik, A.S. Cacciatore, V.G. Contessoto, R.G.H.P. van Heesbeen, B. van den Broek, A.N. Mhaskar, H. Teunissen, B.G. St Hilaire, D. Weisz, A.D. Omer, M. Pham, Z. Colaric, Z.Z. Yang, S.S.P. Rao, N. Mitra, C. Lui, W.J. Yao, R. Khan, L.L. Moroz, A. Kohn, J. St Leger, A. Mena, K. Holcroft, Maria Cristina Gambetta, F.B.A. Lim, E. Farley, N. Stein, A. Haddad, D. Chauss, A.S. Mutlu, M.C. Wang, N.D. Young, E. Hildebrandt, H.H. Cheng, C.J. Knight, T.L.U. Burnham, K.A. Hovel, A.J. Beel, P.J. Mattei, R.D. Kornberg, W.C. Warren, G. Cary, J.L. Gomez-Skarmeta, V. Hinman, K. Lindblad-Toh, F. Di Palma, K. Maeshima, A.S. Multani, Sen Pathak, L. Nel-Themaat, R.R. Behringer, P. Kaur, R.H. Medema, B. van Steensel, E. de Wit, J.N. Onuchic, M. Di Pierro, E.L. Aiden & B.D. Rowland

Science 2021 · DOI / WOSUID

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

Anjali Kaushal, Giriram Mohana, Julien Dorier, Isa Özdemir, Arina Omer, Pascal Cousin, Anastasiia Semenova, Michael Taschner, Oleksandr Dergai, Flavia Marzetta, Christian Iseli, Yossi Eliaz, David Weisz, Muhammad Saad Shamim, Nicolas Guex, Erez Lieberman Aiden & Maria Cristina Gambetta

Nature Communications 2021 · DOI / WOSUID

Graphical abstract

ctcf-loss-abstract
  • Neurons are the only cell type in which CTCF is essential for fly viability.
  • CTCF critically impacts expression patterns of several genes near CTCF sites in the central nervous system.
  • CTCF’s ability to interact with cohesin and form TAD boundaries is conserved in flies and mammals.
  • But whereas CTCF is required to form a large fraction of TAD boundaries in mammals, it is only required to form about 10% of boundaries in flies.
  • This demonstrates that although domain formation is ubiquitous in different species, the contributions of different mechanisms can vary widely.
  • CTCF recruits another insulator protein called Cp190 to all CTCF binding sites.
  • Mere binding of CTCF to DNA is insufficient to regulate a subset of genes near boundaries, which also critically rely on Cp190.
  • CTCF therefore functionally cooperates with a stably bound regulatory cofactor, expanding the view of how CTCF may impact gene regulation.

The Role of Insulation in Patterning Gene Expression

Isa Özdemir & Maria Cristina Gambetta

Genes 2019 · PMID / PMC / DOI

Graphical abstract

the-role-of-insulation-abstract
  • In flies and mammals, dedicated DNA elements (insulators) recruit protein factors (insulator binding proteins, or IBPs) to shield promoters from regulatory elements.
  • In mammals, a single IBP called CCCTC-binding factor (CTCF) is known, whereas genetic and biochemical analyses in Drosophila identified a larger repertoire of IBPs.
  • Insulators are thought to fold chromosomes into conformations that affect regulatory element-promoter communication.
  • Comparing and contrasting observations in flies and mammals reveal that these species have different requirements for insulation, but that insulation is a conserved and critical gene regulation strategy.

The Insulator Protein CTCF Is Required for Correct Hox Gene Expression, but Not for Embryonic Development in Drosophila

Maria Cristina Gambetta & Eileen E M Furlong

Genetics 2018 · PMID / PMC / DOI

Graphical abstract

the-insulator-protein-abstract
  • In stark contrast to mammalian cells that die without CTCF, flies lacking zygotic CTCF survive to adults with homeotic defects.
  • The lack of major embryonic defects was assumed to be due to the maternal supply of CTCF protein, that could rescue the early development of CTCF mutants.
  • Here, we generated animals that completely lack both maternal and zygotic CTCF and found that, contrary to expectation, these mutants progress through embryogenesis and larval life. They develop to pharate adults, which fail to eclose from their pupal case.
  • These mutants show exacerbated homeotic defects compared to zygotic mutants, misexpressing the HOX gene Abdominal-B outside of its normal expression domain early in development.
  • This indicates that loss of Drosophila CTCF is not accompanied by widespread effects on gene expression, which may be due to redundant functions with other insulator proteins.
  • Rather, CTCF is required for correct HOX gene expression patterns and for the viability of adult Drosophila.

A critical perspective of the diverse roles of O-GlcNAc transferase in chromatin

Maria Cristina Gambetta & Jürg Müller

Chromosoma 2015 · PMID / PMC / DOI

Graphical abstract

a-critical-perspective-abstract
  • O-linked β-N-Acetylglucosamine (O-GlcNAc) is a posttranslational modification that is catalyzed by O-GlcNAc transferase (Ogt) and found on a plethora of nuclear and cytosolic proteins in animals and plants.
  • Studies in different model organisms revealed that while O-GlcNAc is required for selected processes in Caenorhabditis elegans and Drosophila, it has evolved to become required for cell viability in mice.
  • Nevertheless, a principal cellular process that engages O-GlcNAcylation in all of these species is the regulation of gene transcription.
  • Here, we revisit several of the primary experimental observations that led to current models of how O-GlcNAcylation affects gene expression.

O-GlcNAcylation prevents aggregation of the Polycomb group repressor polyhomeotic

Maria Cristina Gambetta & Jürg Müller

Developmental cell 2014 · PMID / DOI

Graphical abstract

O-GlcNAcylation-abstract
  • The glycosyltransferase Ogt adds O-linked N-Acetylglucosamine (O-GlcNAc) moieties to nuclear and cytosolic proteins.
  • Drosophila embryos lacking Ogt protein arrest development with a remarkably specific Polycomb phenotype, arising from the failure to repress Polycomb target genes.
  • The Polycomb protein Polyhomeotic (Ph), an Ogt substrate, forms large aggregates in the absence of O-GlcNAcylation both in vivo and in vitro.
  • O-GlcNAcylation of a serine/threonine (S/T) stretch in Ph is critical to prevent nonproductive aggregation of both Drosophila and human Ph via their C-terminal sterile alpha motif (SAM) domains in vitro.
  • Full Ph repressor activity in vivo requires both the SAM domain and O-GlcNAcylation of the S/T stretch.
  • Ph mutants lacking the S/T stretch reproduce the phenotype of ogt mutants, suggesting that the S/T stretch in Ph is the key Ogt substrate in Drosophila.
  • We propose that O-GlcNAcylation is needed for Ph to form functional, ordered assemblies via its SAM domain.

Structural basis for targeting the chromatin repressor Sfmbt to Polycomb response elements

Claudio Alfieri, Maria Cristina Gambetta, Raquel Matos, Sebastian Glatt, Peter Sehr, Sven Fraterman, Matthias Wilm, Jürg Müller & Christoph W. Müller

Genes & development 2013 · PMID / PMC / DOI

Graphical abstract

structural-basis-abstract
  • Polycomb group (PcG) protein complexes repress developmental regulator genes by modifying their chromatin.
  • Here, we report the crystal structure of the core of the Drosophila PcG protein complex Pleiohomeotic (Pho)repressive complex (PhoRC), which contains the Polycomb response element (PRE)-binding protein Pho and Sfmbt.
  • The spacer region of Pho, separated from the DNA-binding domain by a long flexible linker, forms a tight complex with the four malignant brain tumor (4MBT) domain of Sfmbt.
  • The highly conserved spacer region of the human Pho ortholog YY1 binds three of the four human 4MBT domain proteins in an analogous manner but with lower affinity.
  • Structure-guided mutations that disrupt the interaction between Pho and Sfmbt abolish formation of a ternary Sfmbt:Pho:DNA complex in vitro and repression of developmental regulator genes in Drosophila.
  • PRE tethering of Sfmbt by Pho is therefore essential for Polycomb repression in Drosophila.

The role of the histone H2A ubiquitinase Sce in Polycomb repression

Luis Gutiérrez, Katarzyna Oktaba, Johanna C. Scheuermann, Maria Cristina Gambetta, Nga Ly-Hartig & Jürg Müller

Development (Cambridge, England) 2011 · PMID / PMC / DOI

Essential role of the glycosyltransferase sxc/Ogt in polycomb repression

Maria Cristina Gambetta, Katarzyna Oktaba & Jürg Müller

Science (New York, N.Y.) 2009 · PMID / DOI

Graphical abstract

essential-role-of-the-glycosyltransferase-abstract
  • Polycomb group proteins are conserved transcriptional repressors that control animal and plant development.
  • Here, we found that the Drosophila Polycomb group gene super sex combs (sxc) encodes Ogt, the highly conserved glycosyltransferase that catalyzes the addition of Nacetylglucosamine (GlcNAc) to proteins in animals and plants.
  • Genome-wide profiling in Drosophila revealed that GlcNAc-modified proteins are highly enriched at Polycomb response elements.
  • Among different Polycomb group proteins, Polyhomeotic is glycosylated by Sxc/Ogt in vivo.
  • sxc/Ogt–null mutants lacked O-linked GlcNAcylation and failed to maintain Polycomb transcriptional repression even though Polycomb group protein complexes were bound at their target sites.
  • Polycomb repression appears to be a critical function of Sxc/Ogt in Drosophila and may be mediated by the glycosylation of Polyhomeotic.

People

Maria Christina Gambetta
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PeriodPositionInstitution
2018-currentTenure-track assistant professorCenter for Integrative Genomics, University of Lausanne, Switzerland
2015-2017Postdoctoral researcherEuropean Molecular Biology Laboratory (EMBL) Heidelberg, Germany
2010-2015Postdoctoral researcherMax Planck Institute of Biochemistry in Martinsried, Germany
2006-2010PhD in BiologyEuropean Molecular Biology Laboratory (EMBL) Heidelberg, Germany
2004-2006M.Sc. BiologyUniversity of Geneva, Switzerland
2001-2004B.Sc. BiologyUniversity of Geneva, Switzerland
OrcID

Maria Cristina Gambetta

Principal Investigator

Iris Marouani

Iris Marouani

Administrative Assistant

Pascal Cousin
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PeriodPositionInstitution
2005 - presentTechnicianCenter for Integrative Genomics, University of Lausanne, Switzerland

Pascal Cousin

Lab Manager

Anastasiia Semenova
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PeriodPositionInstitution
2017 - 2019M.Sc. BiologyTaras Shevchenko National University of Kyiv, ESC Institute of Biology and Medicine, Kyiv, Ukraine
2013 - 2017B.Sc. BiologyTaras Shevchenko National University of Kyiv, ESC Institute of Biology and Medicine, Kyiv, Ukraine

Anastasiia Semenova

PhD Student

Bihan Wang
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PeriodPositionInstitution
2017 - 2018M.Sc. BiochemistryUniversity of Florida, USA
2010 - 2014B.Sc.Wuhan University, School of Pharmaceutical Science, China

Bihan Wang

PhD Student

Marion Mouginot
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PeriodPositionInstitution
2018 - 2020M.Sc. Cellular and Molecular BiologyLyon 1 University, France
2016 - 2018Assistant engineerÉcole Normale Supérieure of Lyon (ENSL), France
2015 - 2016B.Sc. Biotechnology speciality GenomicsLyon 1 University, France
2013 - 2015Technical degree in BiotechnologyMartinière Duchère high school, France
OrcID

Marion Mouginot

PhD Student

Sanyami Zunjarrao
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PeriodPositionInstitution
2019 - 2021Project AssistantNational Chemical Laboratory, India
2014 - 2019M.Sc.Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, India

Sanyami Zunjarrao

PhD Student

Jenisha Khadka
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PeriodPositionInstitution
2020 - 2022 Research InternMax-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
2018 - 2021M.Sc. in Molecular Life SciencesFriedrich-Schiller-Universität Jena, Jena, Germany
2013 - 2017B.Sc. in BiotechnologyPurbanchal University, Kathmandu, Nepal

Jenisha Khadka

PhD Student

Héléna Malek
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PeriodPositionInstitution
2021-present M. Sc. GeneticsUniversity of Paris, France
2020-2021 B. Sc. BiologyUniversity of Paris, France

Héléna Malek

Master Student

Jonas Barraud
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PeriodPositionInstitution
2019-present Apprentice Technician CIG

Jonas Barraud

Lab Technician

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NamePositionAfterInstitution
Giriram MohanaPostdocScientific OfficerCellzome Heidelberg
Anjali KaushalPhD studentNGS scientistSophia genetics
Daniel RodriguezM. Sc.PhD studentFMI Basel
Tasniem FetianInternPhD studentUniversity of Pittsburgh

Contact

Prof. Maria Cristina Gambetta
Center for Integrative Genomics (CIG)
University of Lausanne
Unil-Sorge district
Genopode building
CH-1015 Lausanne
Switzerland

mariacristina.gambetta [at] unil.ch
Office: Room 3030
Phone: +41 21 692 3985

Joining

Are you interested in investigating basic mechanisms of gene regulation specificity?

We are looking for talented and enthusiastic team members at any level with a background in molecular biology, genetics, genomics or imaging. You are eager to engage in scientific discussions, capable of working in a team as well as independently.

Our lab is hosted at the Center for Integrative Genomics (CIG) at the University of Lausanne (UNIL), a vibrant, well-funded institute with a focus on functional genomics and equipped with modern core facilities. We are embedded in the broader Lausanne research environment that includes two universities (UNIL, EPFL), the Swiss Institute of Bioinformatics, Ludwig Center for Cancer Research, University Hospital, and a cluster of biotech companies flourishing in the larger lake Geneva area. We tightly network with other gene regulation labs at UNIL and EPFL, and collaborate with the on-site Bioinformatics Competence Center. There are regular possibilities to present and participate in local or international conferences and workshops. Hard and soft skill, and career development courses are offered on campus. We offer a nice working place in a multicultural, diversified and dynamic academic environment. PhD students will enroll in the UNIL Doctoral Program in Quantitative Biology.

Spontaneous applications are welcome anytime for Master’s/PhD/postdoc fellowships, while fully-funded positions are advertised below.

To apply or request more information, email mariacristina.gambetta [at] unil.ch. Provide your CV, a brief description of your research experience, and why you think your research interests complement ours.

We encourage applications from minorities.

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