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

Associate Professor, 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
 : Plankton and algal responses to environmental fluctuations


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 stress research.

Recent evidence suggests that key cellular regulatory elements could be of different nature than what the central dogma of molecular biology may seem to suggest, 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) in marine microalgae, with a particular focus on their roles in the response to nutrient fluctuations in diatoms.

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 marine 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 noncoding fraction of the genome we have recently identified thousands of lncRNAs (lincRNAs and lncNATs). 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) and hyposalinity stress (Debit, Charton et al., 2023). Although expressed at lower levels than mRNAs, lncRNAs show a well defined cell-type expression specific signature in the three distinct morphotypes of P. tricornutum (Debit, Charton et al., 2023).

Figure 2.
Coding and noncoding transcripts responsive to phosphate (Pi) fluctuations in the marine diatom P. tricornutum. Coding, mRNA (messenger RNAs) ; Noncoding, lncNAT (long noncoding natural antisense RNAs), lincRNA (long intergenic noncoding RNAs). P4, 4 days Pi stress ; P8, 8 days phosphate stress ; U, up-regulated ; R4, 4 days Pi resupply after 4 days Pi stress ; D, down-regulated or =, unchanged transcripts. (Cruz de Carvalho and 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.

We have recently developed a MetaTool to predict lncRNAs in a species-independent way and used it across 414 marine plankton species from 9 different phyla. The full dataset is available as a user-friendly, open-access web interface, LncPlankton.

As an associate professor at UPEC I am also involved in giving lectures to university students in the Life Sciences. The lectures I deliver range from Molecular Biology and Cellular Biology to second (L2) and third (L3) year undergraduate students to Epigenomics and Noncoding RNA Functions to Master students (M1, M2). I have also co-directed the PhD preparation of three graduate students and directed several Masters students. Additionally, I have provided research training and mentoring to 20+ undergraduate students.

Finally, in recent years I’ve become increasingly involved in scientific mediation and outreach activities through talks and round tables, as well as through hands-on activities, for and with the general public, including younger audiences. The aim is to encourage scientific curiosity and to bring closer to the general public the science done in the lab. I am particularly drawn to the intersection of Art & Science, which taps into an innate, sensorial potential that can reach a wide audience.

Selected Awards and Grants
2025-2026 PHC-Sakura, France-Japan (Coordinator with Y. Matsuda)
2024-2028 ANR PRC BrownLincs (Coordinator)
2020-2024 ANR PRC DiaLincs (Coordinator)
2012-2015 Marie Curie IOF (EU, FP7). Rockefeller University (USA) - CNRS/IBENS (FR)