After receiving a diploma in biochemistry from the University of Tübingen (Germany), David Gatfield worked for his PhD thesis on mechanisms of mRNA transport and degradation with Elisa Izaurralde at EMBL Heidelberg (Germany). During his post-doctoral training 2004-2010 with Ueli Schibler at the University of Geneva (Switzerland) he developed a dual interest in circadian clocks and RNA biology. He joined the CIG as a Swiss National Science Foundation Professor in November 2010. Since February 2017, he is Associate Professor at the CIG.
Keywords: circadian clocks, RNA, post-transcriptional regulation of gene expression, translation, ribosomes, metabolism
INTERVIEWRESEARCH REPORT 2015-2016
Research summary
Research in our group combines two scientific themes, circadian clocks and RNA biology.
Using mice and cells, we study how post-transcriptional mechanisms regulate rhythmic gene expression and physiology. In a more general sense, we view circadian rhythms as an excellent paradigm for differential gene expression (with different physiological states naturally given, just spaced by a few hours) that is amenable to studies all the way from the biochemical to the behavioural level, and that is closely linked to health-relevant topics such as metabolism, sleep, hormonal activity, and many more. Post-transcriptional control has been poorly explored in the circadian field so far, and likely provides explanations to some of the enigmas in chronobiology. In return, the circadian field may also serve to uncover general principles of gene expression regulation.
Over the last 5 years, a particular focus of the lab’s activities has been on translation, i.e. the biosynthesis of protein from messenger RNA, carried out by the ribosome. This interest was initially sparked by around-the-clock ribosome profiling experiments that aimed at quantifying daily changes in translation rates in mouse liver. An important question we are trying to address is: what are the mechanisms that allow certain transcripts to be translated and produce protein preferentially at certain times of the day, while the majority of mRNAs appears to be indifferent to time signals? And what is the relevance of this regulation for healthy physiology?
We like to leave room for serendipity and chance – and this is how we have recently wandered from our chronobiological questions back to more basic RNA research. Currently, high-interest topics in the lab include studying the mechanisms by which the so-called upstream open reading frames (uORFs) regulate gene expression output, and understanding the poorly explored phenomenon of ribosomal collisions during translation elongation.
Representative publications
Arpat AB, Liechti A, De Matos M, Dreos R, Janich P, Gatfield D. (2020) Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing. Genome Research 30;985-999.
Tuck AC, Rankova A, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, Castelo-Szekely V, Gatfield D, Bühler M. (2020) Mammalian RNA decay pathways are highly specialized and widely linked to translation. Molecular Cell 77;1222-1236.
Castelo-Szekely V, De Matos M, Tusup M, Pascolo S, Ule J, Gatfield D. (2019) Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock. Nucleic Acids Research 47:5193-209.
Castelo-Szekely V, Arpat AB, Janich P, Gatfield D. (2017) Translational contributions to tissue specificity in rhythmic and constitutive gene expression. Genome Biology 18:116.
Sinturel F, Gerber A, Mauvoisin D, Wang J, Gatfield D, Stubblefield JJ, Green CB, Gachon F, Schibler U. (2017) Diurnal Oscillations in Liver Mass and Cell Size Accompany Ribosome Assembly Cycles. Cell 169:651-63.
Janich P, Arpat AB, Castelo-Szekely V, Lopes M, Gatfield D. (2015) Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames. Genome Research 25:1848-59.
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Mara De Matos - Technician |
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Georgia Katsioudi - PhD Student Georgia graduated from the University of Crete, Greece with a bachelor’s degree in Molecular Biology and Biotechnology and received her master degree in Fundamental Neurosciences from Maastricht University, the Netherlands. During her master thesis she worked at the academic hospital of Copenhagen investigating the role of epigenetic modifications in narcolepsy. After her studies, she joined UNIL for an internship in sleep research and now she is joining Prof Gatfield’s group as a PhD student. |
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René Dreos - Bio-informatician René Dreos joined Prof. Gatfield’s group in August 2018 as a bioinformatician. He has a background in Biology: he graduated in Molecular biology from the University of Trieste (Italy) and did a joint PhD in Nanotechnology at the John Innes Centre (UK). Then he stayed at the JIC to work as a bioinformatician under the supervision of Dr. Wigge where he analyzed gene expression data in A. thaliana. He then moved to Lausanne in Dr. Bucher’s lab (EPFL) where he studied promoter features such as chromatin, transcription factor binding sites, SNPs and DNA motifs in Eukaryotic organisms. Now, at the UNIL, he is the bioinformatician of the NCCR RNA and Disease groups of the Leman lake area (Lausanne and Geneva). |
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Hima Priyanka Nadimpalli - Post-doctoral Fellow Hima comes from India, where she did her Master’s in Biochemistry and Molecular Biology at Pondicherry University. She then moved to Barcelona in 2013 for her PhD at the Centre for Genomic Regulation (CRG) in the group of Fátima Gebauer. During her PhD, she investigated the novel function of siRNA factor Dicer-2 in cytoplasmic polyadenylation of mRNAs in Drosophila. She moved to Lausanne in March for her postdoc and she will investigate the molecular mechanisms and physiological consequences of daily rhythms in protein synthesis and their connections to the circadian clock. |
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Romane Meurs - PhD Student Romane did her master internship in David Gatfield’s lab at the end of the spring semester and now she is back to CIG as a PhD student. She is from Belgium, where she did her bachelor and masters’ degrees. She graduated recently in biochemistry and molecular and cellular biology from the Université Libre de Bruxelles. During her PhD, she will first continue her internship project which is about translational regulatory function of the non-conventional translation factor eIF2D and its link with the circadian rhythm. |
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Sébastien Chamois - Post-doctoral Fellow My name is Sébastien Chamois and I recently arrived in Lausanne after eight years as a student at Sorbonne University in Paris. During these years, I developed a high interest for the study of gene expression and RNA regulation that motivated me to obtain a master’s degree in Molecular and Cellular Biology. I then joined, for my doctoral research, Dr Lionel Benard’s group (Paris) to study the degradation of altered mRNA by a cytoplasmic surveillance pathway (No Go Decay pathway) in Saccharomyces cerevisiae. I discovered that the same enthusiasm towards RNA biology was shared by the Gatfield’s group that I am now grateful to join as a postdoc. At the CIG, I will study natural ribosome pausing and its importance for gene expression.
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Enes Arpa - MD-PhD Student I am Enes Salih Arpa, from Turkey. I am a medical doctor who graduated from Istanbul University Cerrahpasa Faculty of Medicine in July 2021. By the beginning of my medical school years, I was very passionate to add a research angle on my clinical knowledge. Therefore I decided to do summer internships in order to improve my research skills. In 2017, I did an internship in Prof. Marie-Catherine Vozenin’s lab in the Radiation Oncology Department of CHUV. Following that year, I spent my summer in Prof. Hans Acha-Orbea’s lab in the Biochemistry Department of UNIL. After these two experiences, I did my third and fourth internships in Prof. Johan Auwerx’s lab in the Life Sciences Department of EPFL. These internship experiences helped me to be involved in various molecular biology projects and enlarge my scientific perspective. That’s why I decided to do an MD-PhD following my graduation. I wanted to focus on RNA biology, in particular the role of some pathways linked to cancer development, during my PhD that could help me to combine my PhD project with clinics in the future. Now, I am very pleased to join Prof. David Gatfield’s lab as an MD-PhD student. I will work on the positive-negative effects of nonsense mediated mRNA decay (NMD) inhibition on cancer formation
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Du NH, Arpat AB, De Matos M, Gatfield D. (2014) MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale. eLife 3:02510.
The supplementary files and data associated to this publication are available at the following URL.
Janich P, Arpat AB, Castelo-Szekely V, Lopes M, Gatfield D. (2015) Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames. Genome Research 25:1849-59.
The supplementary files and data associated to this publication are available at the following URL.
Castelo-Szekely V, Arpat AB, Janich P, Gatfield D. (2017) Translational contributions to tissue specificity in rhythmic and constitutive gene expression. Genome Biology 18:116.
The supplementary files and data associated to this publication are available at the following URL.
