32 research outputs found
The role of the peptidyl prolyl isomerase Rrd1 in the transcriptional stress response
La régulation de la transcription est un processus complexe qui a évolué pendant des millions
dâannĂ©es permettant ainsi aux cellules de sâadapter aux changements environnementaux. Notre
laboratoire étudie le rÎle de la rapamycine, un agent immunosuppresseur et anticancéreux, qui
mime la carence nutritionelle. Afin de comprendre les mécanismes impliqués dans la réponse a
la rapamycine, nous recherchons des mutants de la levure Saccaromyces cerevisiae qui ont un
phenotype altérée envers cette drogue. Nous avons identifié le gÚne RRD1, qui encode une
peptidyl prolyl isomérase et dont la mutation rend les levures trÚs résistantes à la rapamycine et il
semble que se soit associé à une réponse transcriptionelle alterée. Mon projet de recherche de
doctorat est dâidentifier le rĂŽle de Rrd1 dans la rĂ©ponse Ă la rapamycine. Tout dâabord nous
avons trouvĂ© que Rrd1 interagit avec lâARN polymĂ©rase II (RNAPII), plus spĂ©cifiquement avec
son domaine C-terminal. En réponse à la rapamycine, Rrd1 induit un changement dans la
conformation du domaine C-terminal in vivo permettant la rĂ©gulation de lâassociation de RNAPII
avec certains gÚnes. Des analyses in vitro ont également montré que cette action est directe et
probablement liĂ©e Ă lâactivitĂ© isomĂ©rase de Rrd1 suggĂ©rant un rĂŽle pour Rrd1 dans la rĂ©gulation
de la transcription. Nous avons utilisé la technologie de ChIP sur micropuce pour localiser Rrd1
sur la majorité des gÚnes transcrits par RNAPII et montre que Rrd1 agit en tant que facteur
dâĂ©longation de RNAPII. Pour finir, des rĂ©sultats suggĂšrent que Rrd1 nâest pas seulement
impliqué dans la réponse à la rapamycine mais aussi à differents stress environnementaux, nous
permettant ainsi dâĂ©tablir que Rrd1 est un facteur dâĂ©longation de la transcription requis pour la
régulation de la transcription via RNAPII en réponse au stress.Transcriptional regulation is a complex process that has evolved over millions of years of
evolution. Cells have to sense environmental conditions and adapt to them by altering their
transcription. Herein, we study the role of rapamycin, an immunosuppressant and anticancer
molecule that mimics cellular starvation. To understand how the action of rapamycin is
mediated, we analyzed gene deletion mutants in the yeast Saccharomyces cerevisiae that have an
altered response to this drug. Deletion of RRD1, a gene encoding a peptidyl prolyl isomerase,
causes strong resistance to rapamycin and this was associated with a role of Rrd1 in the
transcriptional response towards rapamycin. The main focus of my PhD was therefore to unravel
the role of Rrd1 in response to rapamycin. First, we discovered that Rrd1 interacts with RNA
polymerase II (RNAPII), more specifically with its C-terminal domain and we showed that in
response to rapamycin, Rrd1 alters the structure of this C-terminal domain. This phenomenon
was confirmed to be directly mediated by Rrd1 in vitro, presumably through its peptidyl prolyl
isomerase activity. Further, we demonstrated that Rrd1 is capable of altering the occupancy of
RNAPII on genes in vivo and in vitro. With the use of ChIP on chip technology, we show that
Rrd1 is actually a transcription elongation factor that is associated with RNAPII on actively
transcribed genes. In addition, we demonstrate that Rrd1 is indeed required to regulate the
expression of a large subset of genes in response to rapamycin. This data let us propose a novel
mechanism by which Rrd1 regulates RNAPII during transcription elongation. Finally, we
provide evidence that Rrd1 is not only required for an efficient response towards rapamycin but
to a larger variety of environmental stress conditions, thus establishing Rrd1 as a transcriptional
elongation factor required to fine tune the transcriptional stress response of RNAPII
The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis
10.1242/dev.131573Development (Cambridge, England)1436950-961GUSTO (Growing up towards Healthy Outcomes
Human granzyme B regulatory B cells prevent effector CD4+CD25- T cell proliferation through a mechanism dependent from lymphotoxin alpha
IntroductionHuman Granzyme B (GZMB) regulatory B cells (Bregs) have suppressive properties on CD4+ effector T cells by a mechanism partially dependent on GZMB. Moreover, these cells may be easily induced in vitro making them interesting for cell therapy.MethodsWe characterized this population of in vitro induced GZMB+Bregs using single cell transcriptomics. To investigate their regulatory properties, Bregs or total B cells were also co-cultured with T cells and scRNAseq was used to identify receptor ligand interactions and to reveal gene expression changes in the T cells.ResultsWe find that Bregs exhibit a unique set of 149 genes differentially expressed and which are implicated in proliferation, apoptosis, metabolism, and altered antigen presentation capacity consistent with their differentiated B cells profile. Notably, Bregs induced a strong inhibition of T cell genes associated to proliferation, activation, inflammation and apoptosis compared to total B cells. We identified and validated 5 receptor/ligand interactions between Bregs and T cells. Functional analysis using specific inhibitors was used to test their suppressive properties and we identified Lymphotoxin alpha (LTA) as a new and potent Breg ligand implicated in Breg suppressive properties.DiscussionWe report for the first time for a role of LTA in GZMB+Bregs as an enhancer of GZMB expression, and involved in the suppressive properties of GZMB+Bregs in human. The exact mechanism of LTA/GZMB function in this specific subset of Bregs remains to be determined
The Peptidyl Prolyl Isomerase Rrd1 Regulates the Elongation of RNA Polymerase II during Transcriptional Stresses
Rapamycin is an anticancer agent and immunosuppressant that acts by inhibiting the TOR signaling pathway. In yeast, rapamycin mediates a profound transcriptional response for which the RRD1 gene is required. To further investigate this connection, we performed genome-wide location analysis of RNA polymerase II (RNAPII) and Rrd1 in response to rapamycin and found that Rrd1 colocalizes with RNAPII on actively transcribed genes and that both are recruited to rapamycin responsive genes. Strikingly, when Rrd1 is lacking, RNAPII remains inappropriately associated to ribosomal genes and fails to be recruited to rapamycin responsive genes. This occurs independently of TATA box binding protein recruitment but involves the modulation of the phosphorylation status of RNAPII CTD by Rrd1. Further, we demonstrate that Rrd1 is also involved in various other transcriptional stress responses besides rapamycin. We propose that Rrd1 is a novel transcription elongation factor that fine-tunes the transcriptional stress response of RNAPII
A histone acetylome-wide association study of Alzheimerâs disease identifies disease-associated H3K27ac differences in the entorhinal cortex
We quantified genome-wide patterns of lysine H3K27 acetylation (H3K27ac) in entorhinal cortex samples from Alzheimerâs disease (AD) cases and matched controls using chromatin immunoprecipitation and highly parallel sequencing. We observed widespread acetylomic variation associated with AD neuropathology, identifying 4,162 differential peaks (false discovery rateâ<â0.05) between AD cases and controls. Differentially acetylated peaks were enriched in disease-related biological pathways and included regions annotated to genes involved in the progression of amyloid-ÎČ and tau pathology (for example, APP, PSEN1, PSEN2, and MAPT), as well as regions containing variants associated with sporadic late-onset AD. Partitioned heritability analysis highlighted a highly significant enrichment of AD risk variants in entorhinal cortex H3K27ac peak regions. AD-associated variable H3K27ac was associated with transcriptional variation at proximal genes including CR1, GPR22, KMO, PIM3, PSEN1, and RGCC. In addition to identifying molecular pathways associated with AD neuropathology, we present a framework for genome-wide studies of histone modifications in complex disease
A complex immune communication between eicosanoids and pulmonary macrophages
International audienceRespiratory viral infections represent a constant threat for human health and urge for a better understanding of the pulmonary immune response to prevent disease severity. Macrophages are at the center of pulmonary immunity, where they play a pivotal role in orchestrating beneficial and/or pathological outcomes during infection. Eicosanoids, the host bioactive lipid mediators, have re-emerged as important regulators of pulmonary immunity during respiratory viral infections. In this review, we summarize the current knowledge linking eicosanoids' and pulmonary macrophages' homeostatic and antimicrobial functions and discuss eicosanoids as emerging targets for immunotherapy in viral infection
Alveolar Macrophages: Adaptation to Their Anatomic Niche during and after Inflammation
At the early stages of life development, alveoli are colonized by embryonic macrophages, which become resident alveolar macrophages (ResAM) and self-sustain by local division. Genetic and epigenetic signatures and, to some extent, the functions of ResAM are dictated by the lung microenvironment, which uses cytokines, ligand-receptor interactions, and stroma cells to orchestrate lung homeostasis. In resting conditions, the lung microenvironment induces in ResAM a tolerogenic programming that prevents unnecessary and potentially harmful inflammation responses to the foreign bodies, which continuously challenge the airways. Throughout life, any episode of acute inflammation, pneumonia being likely the most frequent cause, depletes the pool of ResAM, leaving space for the recruitment of inflammatory monocytes that locally develop in monocyte-derived alveolar macrophages (InfAM). During lung infection, the local microenvironment induces a temporary inflammatory signature to the recruited InfAM to handle the tissue injury and eliminate the pathogens. After a few days, the recruited InfAM, which locally self-sustain and develop as new ResAM, gain profibrotic functions required for tissue healing. After the complete resolution of the infectious episode, the functional programming of both embryonic and monocyte-derived ResAM remains altered for months and possibly for the entire life. Adult lungs thus contain a wide diversity of ResAM since every infection brings new waves of InfAM which fill the room left open by the inflammatory process. The memory of these innate cells called trained immunity constitutes an immunologic scar left by inflammation, notably pneumonia. This memory of ResAM has advantages and drawbacks. In some cases, lung-trained immunity offers better defense capacities against autoimmune disorders and the long-term risk of infection. At the opposite, it can perpetuate a harmful process and lead to a pathological state, as is the case among critically ill patients who have immune paralysis and are highly susceptible to hospital-acquired pneumonia and acute respiratory distress syndrome. The progress in understanding the kinetics of response of alveolar macrophages (AM) to lung inflammation is paving the way to new treatments of pneumonia and lung inflammatory process
Deciphering Transcriptional Networks during Human Cardiac Development
Human heart development is governed by transcription factor (TF) networks controlling dynamic and temporal gene expression alterations. Therefore, to comprehensively characterize these transcriptional regulations, day-to-day transcriptomic profiles were generated throughout the directed cardiac differentiation, starting from three distinct human- induced pluripotent stem cell lines from healthy donors (32 days). We applied an expression-based correlation score to the chronological expression profiles of the TF genes, and clustered them into 12 sequential gene expression waves. We then identified a regulatory network of more than 23,000 activation and inhibition links between 216 TFs. Within this network, we observed previously unknown inferred transcriptional activations linking IRX3 and IRX5 TFs to three master cardiac TFs: GATA4, NKX2-5 and TBX5. Luciferase and co-immunoprecipitation assays demonstrated that these five TFs could (1) activate each otherâs expression; (2) interact physically as multiprotein complexes; and (3) together, finely regulate the expression of SCN5A, encoding the major cardiac sodium channel. Altogether, these results unveiled thousands of interactions between TFs, generating multiple robust hypotheses governing human cardiac development
Deciphering transcriptional networks during human cardiac development
Abstract Human heart development is governed by transcription factor (TF) networks controlling dynamic and temporal gene expression alterations. Therefore, to comprehensively characterize these transcriptional regulations, day-to-day transcriptomic profiles were generated throughout the directed cardiac differentiation, starting from three distinct human induced pluripotent stem cell lines from healthy donors (32 days). We applied an expression-based correlation score to the chronological expression profiles of the TF genes, and clustered them into 12 sequential gene expression waves. We then identified a regulatory network of more than 23 000 activation and inhibition links between 216 TFs. Within this network, we observed previously unknown inferred transcriptional activations linking IRX3 and IRX5 TFs to three master cardiac TFs: GATA4, NKX2-5 and TBX5. Luciferase and co-immunoprecipitation assays demonstrated that these 5 TFs could (1) activate each otherâs expression, (2) interact physically as multiprotein complexes and (3) together, finely regulate the expression of SCN5A , encoding the major cardiac sodium channel. Altogether, these results unveiled thousands of interactions between TFs, generating multiple robust hypotheses governing human cardiac development