AgreenSkills session, year: 2nd session, 2014
Receiving laboratory: Scott Michaels’ lab, Department of Biology, Indiana University , usa
Country of origin : USA
PolII pausing and epigenetic regulation of transcription in Arabidopsis
The precise and coordinated regulation of gene expression, as well as its epigenetic maintenance during cell divisions, is central to the development of the organism and its response to stimuli from the environment. Recently, RNA Polymerase II (PolII) pausing has been shown to play important roles in gene expression, RNA processing and chromatin organization in animals. Evidence that PolII pausing also occurs in plants is still lacking. Based on encouraging preliminary results from Scott Michaels’ group, we will evaluate if PolII pausing occurs in Arabidopsis thaliana and how it could interact with transcriptional and epigenetic mechanisms using genome-wide approaches and bioinformatics.
After obtaining my diploma of engineering in agronomy and my master degree (MSc) at Agrocampus Ouest (2000), I was awarded a PhD scholarship to study transcriptional regulation by nuclear receptors (PPARalpha and RXR) using gene expression microarrays and knockout mouse models in the group of Thierry Pineau. I obtained an INRA permanent staff position (IR2, research engineer) during my PhD studies (2004) and I co-directed the group of Integrative Toxicology & Metabolism for 4 years (2007-2011). I next created the GeT-TRiX transcriptomic core facility at INRA ToxAlim (Research Center in Food Toxicology; 2011-2013).During these years, I led as first (Martin et al., 2005 & 2007), last and/or corresponding author (Marmugi et al., 2012; Roques et al., 2013), as well as PhD supervisor (Eveillard et al., 2009a, 2009b) significant research projects that contributed to the development of ToxAlim. In 2013-2015, I joined the group of Olivier Cuvier, where I studied chromatin organization and transcription in Drosophila cells using various genome-wide approaches based on high throughput sequencing (NGS). Throughout my career, I have balanced biology with bioinformatics and biostatistics and gained experience in the analysis of different types of microarray and NGS data using R/Bioconductor which I share through training sessions. My current research interests focus on studying, at the genome-wide level, the links between RNA Polymerase II pausing/RNA processing with chromatin organization. I am also interested in learning new computational tools to analyze and integrate high-throughput genomic data.
- Stadelmayer B, Micas G, Gamot A, Martin P, Malirat N, Koval S, Raffel R, Sobhian B, Severac D, Rialle S, Parrinello H, Cuvier O, Benkirane M. (2014) Integrator complex regulates NELF-mediated RNA Polymerase II pause/release and processivity at coding genes. Nature Communications. 5:5531
- Roques BB, Leghait J, Lacroix MZ, Lasserre F, Pineau T, Viguié C, Martin PG. (2013) The nuclear receptors pregnane X receptor and constitutive androstane receptor contribute to the impact of fipronil on hepatic gene expression linked to thyroid hormone metabolism. Biochem Pharmacol. 86(7):997-1039
- Marmugi A, Ducheix S, Lasserre F, Polizzi A, Paris A, Priymenko N, Bertrand-Michel J, Pineau T, Guillou H, Martin PG, Mselli-Lakhal L. (2012) Low doses of bisphenol A induce gene expression related to lipid synthesis and trigger triglyceride accumulation in adult mouse liver. Hepatology. 55(2):395-407.
- Eveillard A, Mselli-Lakhal L, Mogha A, Lasserre F, Polizzi A, Pascussi JM, Guillou H, Martin PGP and Pineau T (2009). Di-(2-ethylhexyl)-phthalate (DEHP) activates the constitutive androstane receptor (CAR): a novel signaling pathway sensitive to phthalates. Biochem Pharmacol. 77(11), 1735-1746.
- Le Cao KA, Martin PG, Robert-Granie C and Besse P (2009). Sparse canonical methods for biological data integration: application to a cross-platform study. BMC Bioinformatics. 10, 34.
- Martin PG, Guillou H, Lasserre F, Dejean S, Lan A, Pascussi JM, Sancristobal M, Legrand P, Besse Pand Pineau T (2007). Novel aspects of PPARalpha-mediated regulation of lipid and xenobiotic metabolism revealed through a nutrigenomic study. Hepatology. 45(3), 767-777.