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Proposition de sujet de thèse à l’appui d’une demande de contrat doctoral 2017-2018
Renseignements relatifs à l’Unité de Recherche :
Label et intitulé : Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-
S1016
Nom et prénom du Directeur : Pierre-Olivier Couraud
Téléphone : 01 40 51 64 57 Télécopie : 01 40 51 64 73
Courriel: Institut Cochin, Inserm U1016-CNRS UMR8104-Université Paris Descartes, 22 rue Méchain,
75014 Paris
Renseignements relatifs à l’Equipe :
Nom de l’Equipe d’Accueil : Computational (Epi-)Genetics of Cancer
Nom et prénom du responsable : Valentina Boeva
Qualité du responsable : CR1 Inserm, chef d’équipe
Téléphone : 01 44 41 23 89
Courriel : Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, 24 rue du
Faubourg Saint-Jacques, 75014 Paris, France
Renseignements relatifs au sujet de thèse :
Nom et prénom du Directeur de thèse (HDR) : Valentina Boeva
Qualité : CR1 Inserm, chef d’équipe
Téléphone : 01 44 41 23 89
Courriel : Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, 24 rue du
Faubourg Saint-Jacques, 75014 Paris, France
Titre du sujet proposé :
(En français) Conséquences et mécanismes des activités génétiques et épigénétiques du facteur de
transcription Spi1/PU.1 dans la leucémogenèse
(En anglais) Consequences and mechanisms of genetic and epigenetic activities of the Spi1/PU.1
transcription factor in leukemogenesis
Département (cocher le département correspondant au sujet de thèse qui n’est pas obligatoirement le
vôtre) :
 Biologie Cellulaire et moléculaire, Physiologie et Physiopathologie
 Immunologie
 Développement Génétique Neurobiologie et Vieillissement
 Infectiologie, Microbiologie
Summary (5 lines maximum) :
The project will decipher specific roles of the transcription factor Spi1/PU.1 in leukemic development. Spi1/PU.1,
over-expressed in leukemia, binds to DNA and RNA and interacts with several proteins involved in epigenetic
regulation, alternative splicing and transcriptional co-factors. The goal of this PhD project is to draw a global view of
the role Spi1/PU.1 in controlling DNA and RNA metabolism and understand how alterations of epigenetic states,
gene transcription and splicing that are due to Spi1/PU.1 overexpression are involved in leukemogenesis.

Proposition de sujet de thèse à l’appui d’une demande de contrat doctoral 2017-2087
Nom, prénom du directeur de l'unité de recherche : Pierre-Olivier Couraud
Numéro de l'unité de recherche (et établissement de rattachement) : Institut Cochin, Inserm U1016,
CNRS UMR 8104, Université Paris Descartes UMR-S1016
Nom, prénom du responsable de l'équipe d'accueil (EAD) : Valentina Boeva
Nom, prénom du directeur de thèse : Valentina Boeva
Titre du sujet de thèse proposé : Consequences and mechanisms of genetic and epigenetic activities
of the Spi1/PU.1 transcription factor in leukemogenesis
Citer 5 mots clés : Epigénétique, Bioinformatique, Cancer, Transcription/Splicing, Leucémie
(key words) Epigenetics, Bioinformatics, Cancer, Transcription/Splicing, Leukemia
Candidat pressenti : X OUI NON
Contenu scientifique du programme de la thèse :
Leukemias are due to the progressive accumulation of mutations in myeloid progenitors. Those
mutations alter epigenetic and splicing factors and proteins of signaling networks controlling proliferation
and growth factor dependency and proteins that affect transcription factors (TFs) controlling cell fate
decisions.
This project aims to understand how TFs act on genetic and epigenetic mechanisms in leukemias.
The project focuses specifically on the role of the TF Spi1/PU.1, overexpressed in leukemia. Spi1/PU.1
binds to DNA and RNA and interacts with several proteins involved in epigenetic regulation, alternative
splicing and transcriptional co-factors. The goal of the project is to draw a global view of the role of
Spi1/PU.1 in controlling DNA and RNA metabolism and how alterations of epigenetics, transcription and
splicing that are due to overexpression of Spi1/PU.1 are involved in leukemogenesis.
Specific objectives:
1) Decipher Spi1/PU.1-RNA interactome via CLIP-seq data analysis
2) Understand mechanisms of Spi1/PU.1-RNA binding via integrative analysis of ChIP-seq and
CLIP-seq datasets for Spi1/PU.1
3) Characterize a link between RNA binding/DNA binding and Spi1/PU.1 function in transcriptome
regulation or splicing via integrative analysis of RNA-seq transcriptome and CLIP-seq data.
4) Determine how Spi1 impacts on histone modification profiles and what are the consequences of
these epigenetic modifications on transcription and splicing
Biological experiments have already been performed and the raw data are available: ChIP-seq and
CLIP-seq experiments with an antibody specific Spi1/PU.1; RNA-seq of Spi1-overexpressing leukemic
cells versus cells in which Spi1/PU.1 expression was knock-downed; ChIP-seq profiles of H3K27me3,
H3K27Ac, H3Ac, H3K4me1, H3K4me3, H3K36me3 and of RNApolII binding sites.
Expected results:
Overall, the integrative analysis of ChIP-seq, RNA-seq and CLIP-seq data is expected to shed light on
the mechanisms of Spi1/PU.1 action on DNA and RNA and elucidate consequences of such binding.
The results, targets and pathways, proposed by the bioinformatics analysis will be validated by
researchers of the group of C. Guillouf, which will perform biological experiments to validate the
predicted mechanisms of the Spi1/PU.1 action in leukemias. Altogether, this work has a potential to
decipher the complexity of the action of a TF at genetic and epigenetic levels in normal and leukemic
context.
Additional information:
The student will work on this project in the laboratory of computationally epigenetics of cancer (PI:
Valentina Boeva), Institut Cochin, Paris, under the co-supervision of Valentina Boeva and Christel
Guillouf (laboratory of normal and pathological haematopoiesis, Institut Gustave Roussy, Villejuif). V.
Boeva team specializes in bioinformatics analysis of cancer high-throughput data and will lead the data
analysis of the project. The team of C. Guillouf brings the biological high-throughput data for this project
and ensures coordination of biological aspects. The two teams will have regular meetings to guarantee
the overall progress of the PhD project. The project is supported by ATIP-AVENIR (Boeva) and PL-BIO

INCa (Guillouf). The laboratory of computationally epigenetics of cancer provides the required equipment
(DELL working station for data analysis and a NAS data storage server) for the completion of the project.
Indiquez les cinq meilleures publications récentes de l’équipe :
Significant papers on the subject of Boeva lab:
 Ashoor,H. et al. (2017) HMCan-diff: a method to detect changes in histone modifications in cells
with different genetic characteristics. Nucleic Acids Res. doi: 10.1093/nar/gkw1319
 Grünewald,T.G.P. et al. (2015) Chimeric EWSR1-FLI1 regulates the Ewing sarcoma
susceptibility gene EGR2 via a GGAA microsatellite. Nat. Genet., 47, 1073–1078.
 da Rocha,S.T. et al. (2014) Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to
the Inactive X Chromosome. Mol. Cell, 53, 301–316.
 Ashoor,H. et al. (2013) HMCan: a method for detecting chromatin modifications in cancer
samples using ChIP-seq data. Bioinformatics, 29, 2979–2986.
 *Boeva V. et al. (2012) Nebula-a web server for advanced ChIP-seq data analysis.
Bioinformatics, 28, 2517-9
Papers related to the subject of Guillouf lab:
 Ridinger-Saison M, Evanno E, Gallais I, Rimmele P, Selimoglu-Buet D, et al. (2013) Epigenetic
silencing of Bim transcription by Spi-1/PU.1 promotes apoptosis resistance in leukaemia. Cell
Death Differ.
 *Ridinger-Saison M, Boeva V, Rimmele P, Kulakovskiy I, Gallais I, et al. (2012) Spi-1/PU.1
activates transcription through clustered DNA occupancy in erythroleukemia. Nucleic Acids Res.
40(18):8927-41.
 Rimmele P, Komatsu J, Hupe P, Roulin C, Barillot E, et al. (2010) Spi-1/PU.1 oncogene
accelerates DNA replication fork elongation and promotes genetic instability in the absence of
DNA breakage. Cancer Res 70: 6757-6766.
* Papers including Boeva and Guillouf