Institut de Biologie de l'École Normale Supérieure ENS . CNRS UMR8197 . Inserm U1024 Directeur : Pierre Paoletti

Maître de Conférences, HDR, UPEC

Contact details

Address : Institut de Biologie de l’Ecole Normale Supérieure (IBENS)
46 rue d’Ulm, 75005 Paris, France
Phone : + (33) 144 32 35 28
E-mail : cruz chez biologie.ens.fr
Google Scholar profile

Research interests
 : Plant and diatom responses to environmental stress


Long noncoding RNAs
The work I have developed so far has enabled me to apprehend the multigenic nature of the environmental stress response of photosynthetic organisms, from land plants to unicellular algae. The physiological adaptation to one given stress factor is ultimately the result of a complex and precise cellular program, triggered by that stress. However, the key genomic elements that orchestrate these stress responses are yet to be found. Identifying these upstream key elements and revealing how they operate in time and space to orchestrate a response that leads to stress adaptation is the ultimate goal of fundamental and applied stress research.
Recent evidence suggests that the cellular key regulatory elements could be of different nature than what the central dogma of molecular biology has established, and that RNA species are far more than simple messengers. Longtime considered as transcriptional noise or artifacts, noncoding RNAs are starting to be recognized as important biological actors in the regulation of cellular processes.
My present research focuses on the identification and functional characterization of regulatory non-protein coding RNA species, namely long noncoding RNAs (lncRNAs).

Figure 1. Long non-protein coding RNAs (lncRNAs) arise from different parts of the genome and are named according to their location in relation to protein coding genes (mRNAs). lincRNAs, intergenic RNAs ; incRNAs, intronic RNAs ; lncNAT (or NATs), RNAs that are transcribed from the opposite strand of a protein-coding gene sequence.

LncRNAs in diatoms
Out of the 55 million nucleotides that make up the genome of the model diatom Phaeodactylum tricornutum, around 19 million correspond to putative protein coding genes (Phatr3). This means that approximately 35% of the genome codes for proteins while the remainder 65% is non-coding. In the non-coding fraction of the genome we have recently identified thousands of lncRNAs (lincRNAs and NATs). These are polyadenylated bona fide discrete transcripts that are expressed under specific stress conditions such as phosphate or nitrogen depletion (Cruz de Carvalho et al., 2016 ; Cruz de Carvalho & Bowler, 2020). My current work involves the functional study of these noncoding genes, namely by the generation of mutant CRISPR-Cas9 and overexpressing lines for the study of the loss-of-function and gain-of-function phenotypes, respectively. I am also characterizing, on a larger scale, the coding and noncoding genome/transcriptome fractions of close to one hundred diatom species and relating this with the ecological and evolutionary relevance of this phytoplankton group.

As an associate professor at UPEC I am also involved in lecturing university students in the Life Sciences. The lectures I deliver range form Plant Botany and Physiology to first year undergraduate students (L1) to Epigenomics and Noncoding RNA Functions to Master students (M2). I have also co-directed the Ph.D. preparation of two graduate students and directed three M2 students, one M1 student and am currently directing a PhD student. Additionally, I have provided research training and mentoring to 15+ undergraduate students.

Selected Awards and Grants
2020-2024 ANR DiaLincs (Coordinator.)
2012-2015 Marie Curie IOF (EU, FP7). Rockefeller University (USA) - CNRS/IBENS (FR)
2010-2011 PHC-Pessoa 22754QL EGIDE, MAE (Ministère des Affaires Etrangères, FR)
2010 Travel Award from ICLGG (USA).
2009-2010 Small Project Grant, UMR CNRS 7618 (FR)
2008 Travel Grant, MAE (FR)
2006-2007 PHC-Pessoa 1127UA EGIDE, MAE (FR)
2003-2004 Post-doctoral Fellowship, FCT (PT)
2001-2003 Post-doctoral Fellowship, FCT (PT)
1996-2000 Ph.D. Fellowship, FCT (PT)