Functional Genomics

Functional Genomics

Support of Next-Generation Sequencing from routine applications to customized solutions

The Functional Genomics team provides state-of-the-art support to FMI scientists for various next-generation sequencing (NGS) applications, from single-cell transcriptomics, epigenomics to whole genome sequencing.

We offer advices on experimental design, perform library preparation for supported applications, and manage NGS sequencing on Illumina platforms. Our laboratory is equipped with Illumina instruments (MiSeq, NextSeq and HiSeq2500), an Agilent Bravo liquid handling robot and a 10X genomics single-cell controller.

In addition, we collaborate with research groups to develop and implement new methods.

Genomics is a very fast evolving research field and we aim to keep at the forefront of the technology and share knowledge with all FMI scientists.

Contact
Sebastien Smallwood: Platform head, functional genomics

Redolfi J, Zhan Y, Valdes-Quezada C, Kryzhanovska M, Guerreiro I, Iesmantavicius V, Pollex T, Grand RS, Mulugeta E, Kind J, Tiana G, Smallwood SA, de Laat W, Giorgetti L (2019) DamC reveals principles of chromatin folding in vivo without crosslinking and ligation.

Nat Struct Mol Biol. 2019 Jun;26(6):471-480

Villegas F, Lehalle D, Mayer D, Rittirsch M, Stadler MB, Zinner M, Olivieri D, Vabres P, Duplomb-Jego L, De Bont ESJM, Duffourd Y, Duijkers F, Avila M, Geneviève D, Houcinat N, Jouan T, Kuentz P, Lichtenbelt KD, Thauvin-Robinet C, St-Onge J, Thevenon J, van Gassen KLI, van Haelst M, van Koningsbruggen S, Hess D, Smallwood SA, Rivière JB, Faivre L, Betschinger J (2019) Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3.

Cell Stem Cell. 2019 Feb 7;24(2):257-270.e8

Peat JR, Smallwood SA (2018) Low Input Whole-Genome Bisulfite Sequencing Using a Post-Bisulfite Adapter Tagging Approach.

Methods Mol Biol. 2018;1708:161-169

Lee HJ, Smallwood SA (2017) Genome-Wide Analysis of DNA Methylation in Single Cells Using a Post-bisulfite Adapter Tagging Approach.

Methods Mol Biol. 2018;1712:87-95

Britschgi A, Duss S, Kim S, Couto JP, Brinkhaus H, Koren S, De Silva D, Mertz KD, Kaup D, Varga Z, Voshol H, Vissieres A, Leroy C, Roloff T, Stadler MB, Scheel CH, Miraglia LJ, Orth AP, Bonamy GM, Reddy VA, Bentires-Alj M (2017) The Hippo kinases LATS1 and 2 control human breast cell fate via crosstalk with ERa.

Nature. 2017 Jan 26;541(7638):541-545

Koren S, Reavie L, Couto JP, De Silva D, Stadler MB, Roloff T, Britschgi A, Eichlisberger T, Kohler H, Aina O, Cardiff RD, Bentires-Alj M (2015) PIK3CA(H1047R) induces multipotency and multi-lineage mammary tumours.

Nature. 2015 Sep 3;525(7567):114-8

Krebs AR, Dessus-Babus S, Burger L, Schübeler D (2014) High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions.

Elife. 2014 Sep 26;3:e04094

Gaidatzis D, Burger L, Murr R, Lerch A, Dessus-Babus S, Schübeler D, Stadler MB (2014) DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes.

PLoS Genet. 2014 Feb;10(2):e1004143

Gurbuz I, Ferralli J, Roloff T, Chiquet-Ehrismann R, Asparuhova MB (2014) SAP domain-dependent Mkl1 signaling stimulates proliferation and cell migration by induction of a distinct gene set indicative of poor prognosis in breast cancer patients.

Mol Cancer. 2014 Feb 5;13:22

Hisano M, Erkek S, Dessus-Babus S, Ramos L, Stadler MB, Peters AH (2013) Genome-wide chromatin analysis in mature mouse and human spermatozoa.

Nat Protoc. 2013 Dec;8(12):2449-70

Gattelli A, Nalvarte I, Boulay A, Roloff TC, Schreiber M, Carragher N, Macleod KK, Schlederer M, Lienhard S, Kenner L, Torres-Arzayus MI, Hynes NE (2013) Ret inhibition decreases growth and metastatic potential of estrogen receptor positive breast cancer cells.

EMBO Mol Med. 2013 Sep;5(9):1335-50

Meier-Abt F, Milani E, Roloff T, Brinkhaus H, Duss S, Meyer DS, Klebba I, Balwierz PJ, van Nimwegen E, Bentires-Alj M (2013) Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium.

Breast Cancer Res. 2013 Apr 29;15(2):R36

Yokobayashi S, Liang CY, Kohler H, Nestorov P, Liu Z, Vidal M, van Lohuizen M, Roloff TC, Peters AH (2013) PRC1 coordinates timing of sexual differentiation of female primordial germ cells.

Nature. 2013 Mar 14;495(7440):236-40

Aceto N, Duss S, MacDonald G, Meyer DS, Roloff TC, Hynes NE, Bentires-Alj M (2012) Co-expression of HER2 and HER3 receptor tyrosine kinases enhances invasion of breast cells via stimulation of interleukin-8 autocrine secretion.

Breast Cancer Res. 2012 Oct 12;14(5):R131

Kueng S, Tsai-Pflugfelder M, Oppikofer M, Ferreira HC, Roberts E, Tsai C, Roloff TC, Sack R, Gasser SM (2012) Regulating repression: roles for the sir4 N-terminus in linker DNA protection and stabilization of epigenetic states.

PLoS Genet. 2012;8(5):e1002727

Posfai E, Kunzmann R, Brochard V, Salvaing J, Cabuy E, Roloff TC, Liu Z, Tardat M, van Lohuizen M, Vidal M, Beaujean N, Peters AH (2012) Polycomb function during oogenesis is required for mouse embryonic development.

Genes Dev. 2012 May 1;26(9):920-32

Lienert F, Mohn F, Tiwari VK, Baubec T, Roloff TC, Gaidatzis D, Stadler MB, Schübeler D (2011) Genomic prevalence of heterochromatic H3K9me2 and transcription do not discriminate pluripotent from terminally differentiated cells.

PLoS Genet. 2011 Jun;7(6):e1002090

Deguchi Y, Donato F, Galimberti I, Cabuy E, Caroni P (2011) Temporally matched subpopulations of selectively interconnected principal neurons in the hippocampus.

Nat Neurosci. 2011 Apr;14(4):495-504

Lempiäinen H, Müller A, Brasa S, Teo SS, Roloff TC, Morawiec L, Zamurovic N, Vicart A, Funhoff E, Couttet P, Schübeler D, Grenet O, Marlowe J, Moggs J, Terranova R (2011) Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice.

PLoS One. 2011 Mar 24;6(3):e18216

Busskamp V, Duebel J, Balya D, Fradot M, Viney TJ, Siegert S, Groner AC, Cabuy E, Forster V, Seeliger M, Biel M, Humphries P, Paques M, Mohand-Said S, Trono D, Deisseroth K, Sahel JA, Picaud S, Roska B (2010) Genetic reactivation of cone photoreceptors restores visual responses in retinitis pigmentosa.

Science. 2010 Jul 23;329(5990):413-7

Bell O, Schwaiger M, Oakeley EJ, Lienert F, Beisel C, Stadler MB, Schübeler D (2010) Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing.

Nat Struct Mol Biol. 2010 Jul;17(7):894-900

Schwaiger M, Kohler H, Oakeley EJ, Stadler MB, Schübeler D (2010) Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome.

Genome Res. 2010 Jun;20(6):771-80

Brykczynska U, Hisano M, Erkek S, Ramos L, Oakeley EJ, Roloff TC, Beisel C, Schübeler D, Stadler MB, Peters AH (2010) Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa.

Nat Struct Mol Biol. 2010 Jun;17(6):679-87

Dey JH, Bianchi F, Voshol J, Bonenfant D, Oakeley EJ, Hynes NE (2010) Targeting fibroblast growth factor receptors blocks PI3K/AKT signaling, induces apoptosis, and impairs mammary tumor outgrowth and metastasis.

Cancer Res. 2010 May 15;70(10):4151-62

Emmerth S, Schober H, Gaidatzis D, Roloff T, Jacobeit K, Bühler M (2010) Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly.

Dev Cell. 2010 Jan 19;18(1):102-13

Tomovic A, Stadler M, Oakeley EJ (2009) Transcription factor site dependencies in human, mouse and rat genomes.

BMC Bioinformatics. 2009 Oct 16;10:339

Gaidatzis D, Jacobeit K, Oakeley EJ, Stadler MB (2009) Overestimation of alternative splicing caused by variable probe characteristics in exon arrays.

Nucleic Acids Res. 2009 Sep;37(16):e107

Matsuda Y, Schlange T, Oakeley EJ, Boulay A, Hynes NE (2009) WNT signaling enhances breast cancer cell motility and blockade of the WNT pathway by sFRP1 suppresses MDA-MB-231 xenograft growth.

Breast Cancer Res. 2009;11(3):R32

Saxena S, Cabuy E, Caroni P (2009) A role for motoneuron subtype-selective ER stress in disease manifestations of FALS mice.

Nat Neurosci. 2009 May;12(5):627-36

Schwaiger M, Stadler MB, Bell O, Kohler H, Oakeley EJ, Schübeler D (2009) Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome.

Genes Dev. 2009 Mar 1;23(5):589-601

Members

Platform/Service Head

Sébastien Smallwood (Platform head, functional genomics)

Technical/Research associates

Sirisha Aluri (Research associate, platform)
Kirsten Jacobeit (Research associate, platform)
Eliza Pandini Figueiredo Moreno (Research associate, platform)
Stéphane Thiry (Research associate, platform)

Alumni

Platform/Service Head

Tim Roloff (2009-2015, Platform head, functional genomics)
Edward Oakeley (2000-2009, Platform head, functional genomics)

PhD students

Andrija Tomovic (2004-2008, PhD student)

Postdoctoral fellows

Magdalena Guzowska (2011-2013, Postdoctoral fellow)
Erik Cabuy (2005-2007, Postdoctoral fellow)

Technical/Research associates

Desiree von Tell (2018, Technical/Research associate)
Birgitte Lucas (2013-2018, Technical/Research associate)
Sophie Dessus-Babus (2010-2015, Technical/Research associate)
Erik Cabuy (2007-2010, Research associate in single cell genomics)
Herbert Angliker (1996-2009, Technical/Research associate)

Biography of Sebastien Smallwood

Software and Tools

Test - Not in use for now