Isabelle Barde

Release of human cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch

Isabelle Barde, Marco Cassano, Suk Min Jang, Adamantia Kapopoulou, Benjamin Rauwel, Didier Trono

Human cytomegalovirus (HCMV) is a highly prevalent pathogen that induces life-long infections notably through the establishment of latency in hematopoietic stem cells (HSC). Bouts of reactivation are normally controlled by the immune system, but can be fatal in immuno-compromised individuals such as organ transplant recipients. Here, we reveal that HCMV latency in human CD34(+) HSC reflects the recruitment on the viral genome of KAP1, a master co-repressor, together with HP1 and the SETDB1 histone methyltransferase, which results in transcriptional silencing. During lytic infection, KAP1 is still associated with the viral genome, but its heterochromatin-inducing activity is suppressed by mTOR-mediated phosphorylation. Correspondingly, HCMV can be forced out of latency by KAP1 knockdown or pharmacological induction of KAP1 phosphorylation, and this process can be potentiated by activating NFkB with TNF-α. These results suggest new approaches both to curtail CMV infection and to purge the virus from organ transplants.

2015

Modulation of mitophagy and use thereof

Isabelle Barde, Didier Trono

The present invention relates to an agent or composition comprising at least one of: (i) a micro-RNA targeting a mitophagy-associated gene or a variant thereof, (ii) a vector comprising a nucleic acid encoding said micro-RNA or variant thereof, (iii) an inducer of said micro-RNA, and (iv) an inhibitor of said micro-RNA, for use as a medicament. In particular, the invention relates to substances and compositions useful in the treatment of mitochondria-related diseases, in a subject, or to enhance protocols of in vitro production of red blood cells.

2014

A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy

Isabelle Barde, Andrea Corsinotti, Adamantia Kapopoulou, Ray Marcel Marin Florez, Sandra Eloise Offner, Benjamin Rauwel, Didier Trono, Jiri Vanicek, Sonia Verp

During hematopoiesis, lineage- and stage-specific transcription factors work in concert with chromatin modifiers to direct the differentiation of all blood cells. Here, we explored the role of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor KAP1 in this process. Hematopoietic-restricted deletion of Kap1 in the mouse resulted in severe hypoproliferative anemia. Kap1-deleted erythroblasts failed to induce mitophagy-associated genes and retained mitochondria. This was due to persistent expression of microRNAs targeting mitophagy transcripts, itself secondary to a lack of repression by stage-specific KRAB-ZFPs. The KRAB/KAP1-miRNA regulatory cascade is evolutionary conserved, as it also controls mitophagy during human erythropoiesis. Thus, a multilayered transcription regulatory system is present, where protein- and RNA-based repressors are superimposed in combinatorial fashion to govern the timely triggering of an important differentiation event.

Amer Assoc Advancement Science2013

KAP1 regulates gene networks controlling mouse B-lymphoid cell differentiation and function

Isabelle Barde, Karolina Bojkowska, Andrea Corsinotti, Nicola Harris, Adamantia Kapopoulou, Sandra Eloise Offner, Didier Trono

Chromatin remodeling is fundamental for B-cell differentiation. In the present study, we explored the role of KAP1, the cofactor of KRAB-ZFP transcriptional repressors, in this process. B-lymphoid-specific Kap1-KO mice displayed reduced numbers of mature B cells, lower steady-state levels of Abs, and accelerated rates of decay of neutralizing Abs after viral immunization. Transcriptome analyses of Kap1-deleted B splenocytes revealed an up-regulation of PTEN, the enzymatic counteractor of PIK3 signaling, and of genes encoding DNA-damage response factors, cell-cycle regulators, and chemokine receptors. ChIP/seq studies established that KAP1 bound at or close to several of these genes and controlled chromatin status at their promoters. Genome wide, KAP1 binding sites lacked active B cell-specific enhancers and were enriched in repressive histone marks, further supporting a role for this molecule in gene silencing in vivo. Likely responsible for tethering KAP1 to at least some of these targets, a discrete subset of KRAB-ZFPs is enriched in B lymphocytes. Our results therefore reveal the role of KRAB/KAP1-mediated epigenetic regulation in B-cell development and homeostasis.

2012

KAP1 regulates gene networks controlling T-cell development and responsiveness

Isabelle Barde, Karolina Bojkowska, Andrea Corsinotti, Nicola Harris, Adamantia Kapopoulou, Sandra Eloise Offner, Didier Trono

Chromatin remodeling at specific genomic loci controls lymphoid differentiation. Here, we investigated the role played in this process by Kruppel-associated box (KRAB)-associated protein 1 (KAP1), the universal cofactor of KRAB-zinc finger proteins (ZFPs), a tetrapod-restricted family of transcriptional repressors. T-cell-specific Kap1-deleted mice displayed a significant expansion of immature thymocytes, imbalances in CD4(+)/CD8(+) cell ratios, and altered responses to TCR and TGFβ stimulation when compared to littermate KAP1 control mice. Transcriptome and chromatin studies revealed that KAP1 binds T-cell-specific cis-acting regulatory elements marked by the H3K9me3 repressive mark and enriched in Ikaros/NuRD complexes. Also, KAP1 directly controls the expression of several genes involved in TCR and cytokine signaling. Among these, regulation of FoxO1 seems to play a major role in this system. Likely responsible for tethering KAP1 to at least part of its genomic targets, a small number of KRAB-ZFPs are selectively expressed in T-lymphoid cells. These results reveal the so far unsuspected yet important role of KAP1-mediated epigenetic regulation in T-lymphocyte differentiation and activation.- Santoni de Sio, F. R., Barde, I., Offner, S., Kapopoulou, A., Corsinotti, A., Bojkowska, K., Genolet, R., Thomas, J. H., Luescher, I. F., Pinschewer, D., Harris, N., Trono, D. KAP1 regulates gene networks controlling T-cell development and responsiveness.

Federation Amer Soc Exp Biol2012

MicroRNA-124 Is a Subventricular Zone Neuronal Fate Determinant

Isabelle Barde, Johan Jakobsson, Didier Trono, Sonia Verp

New neurons are continuously generated from neural stem cells with astrocyte properties, which reside in close proximity to the ventricle in the postnatal and adult brain. In this study we found that microRNA-124 (miR-124) dictates postnatal neurogenesis in the mouse subventricular zone. Using a transgenic reporter mouse we show that miR-124 expression is initiated in the rapid amplifying progenitors and remains expressed in the resulting neurons. When we stably inhibited miR-124 in vivo, neurogenesis was blocked, leading to the appearance of ectopic cells with astrocyte characteristics in the olfactory bulb. Conversely, when we overexpressed miR-124, neural stem cells were not maintained in the subventricular zone and neurogenesis was lost. In summary, our results demonstrate that miR-124 is a neuronal fate determinant in the subventricular zone.

Society for Neuroscience2012

The Kruppel-associated Box Repressor Domain Can Induce Reversible Heterochromatization of a Mouse Locus in Vivo

Isabelle Barde, Anna Claire Groner, Sandra Eloise Offner, Didier Trono, Sonia Verp

The study of chromatin and its regulators is key to understanding and manipulating transcription. We previously exploited the Krüppel-associated box (KRAB) transcriptional repressor domain, present in hundreds of vertebrate-specific zinc finger proteins, to assess the effect of its binding to gene bodies. These experiments revealed that the ectopic and doxycycline (dox)-controlled tet repressor KRAB fusion protein (tTRKRAB) can induce reversible and long-range silencing of cellular promoters. Here, we extend this system to in vivo applications and use tTRKRAB to achieve externally controllable repression of an endogenous mouse locus. We employed lentiviral-mediated transgenesis with promoterless TetO-containing gene traps to engineer a mouse line where the endogenous kinesin family member 2A (Kif2A) promoter drives a YFP reporter gene. When these mice were crossed to animals expressing the TetO-binding tTRKRAB repressor, this regulator was recruited to the Kif2A locus, and YFP expression was reduced. This effect was reversed when dox was given to embryos or adult mice, demonstrating that the cellular Kif2A promoter was only silenced upon repressor binding. Molecular analyses confirmed that tTRKRAB induced transcriptional repression through the spread of H3K9me3-containing heterochromatin, without DNA methylation of the trapped Kif2A promoter. Therefore, we demonstrate that targeting of tTRKRAB to a gene body in vivo results in reversible transcriptional repression through the spreading of facultative heterochromatin. This finding not only sheds light on KRAB-mediated transcriptional processes, but also suggests approaches for the externally controllable and reversible modulation of chromatin and transcription in vivo.

2012

Isabelle Barde

The questions you should ask yourself for efficient CRISPR/Cas9 genome editing

Release of human cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch

Control of mitophagie by microRNAs - A key step of erythropoiesis

Modulation of mitophagy and use thereof

A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy

KAP1 regulates gene networks controlling mouse B-lymphoid cell differentiation and function

KAP1 regulates gene networks controlling T-cell development and responsiveness

MicroRNA-124 Is a Subventricular Zone Neuronal Fate Determinant

The Kruppel-associated Box Repressor Domain Can Induce Reversible Heterochromatization of a Mouse Locus in Vivo

The questions you should ask yourself for efficient CRISPR/Cas9 genome editing

Release of human cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch

Modulation of mitophagy and use thereof

KAP1 regulates gene networks controlling mouse B-lymphoid cell differentiation and function

Control of mitophagie by microRNAs - A key step of erythropoiesis

A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy

KAP1 regulates gene networks controlling T-cell development and responsiveness

MicroRNA-124 Is a Subventricular Zone Neuronal Fate Determinant

The Kruppel-associated Box Repressor Domain Can Induce Reversible Heterochromatization of a Mouse Locus in Vivo