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Helena Cruz de Carvalho

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
Google Scholar profile

Research interests
 : Plant and (micro)algae 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 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) 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 v1.0.

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 form Molecular Biology and Cellular Biology to second (L2) and third (L3) undergraduate students to Epigenomics and Noncoding RNA Functions to Master students (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 15+ undergraduate students.

Selected Awards and Grants
2024-2028 ANR BrownLincs (Coordinator)
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)
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)

Selected publications

• Light-dependent signal transduction in the marine diatom Phaeodactylum tricornutum. Agarwal A, Levitan O, Cruz de Carvalho H, Falkowski PG (2023). PNAS 120 (11) e2216286120.

• Differential expression patterns of long noncoding RNAs in a pleiomorphic diatom and relation to hyposalinity. Debit A*, Charton F*, Pierre-Elies P, Bowler C, Cruz de Carvalho H (2023).*equal contribution Scientific Reports 13 : 2440.

• Dynamic Cell Imaging : application to the diatom Phaeodactylum tricornutum under environmental stresses. Bey H, Charton F, Cruz de Carvalho H, Liu S, Dorrell RG, Bowler C, Boccara M, Boccara C (2022). European Journal of Phycology

• Global identification of a marine diatom long noncoding natural antisense transcripts (NATs) and their response to phosphate fluctuations. Cruz de Carvalho MH, Bowler C (2020). Scientific Reports 10 : 14110.

• A potential role for epigenetic processes in the acclimation response to elevated pCO2 in the model diatom Phaeodactylum tricornutum. Huang R, Ding J, Gao K, Cruz de Carvalho MH, Tirichine L, Bowler C, Lin X (2019). Frontiers in Microbiology 9 : 3342.

• Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations. Cruz de Carvalho MH, Sun H-X, Bowler C, Chua N-H (2016). New Phytologist 210 : 497–510.

• Global reprogramming of transcription and metabolism in Medicago truncatula during progressive drought and after re‐watering. Zhang JY, Cruz de Carvalho MH, Torres-Jerez I, Kang Y, Allen SN, Huhman DV, Tang Y, Murray J, Sumner LW, Udvardi MK (2014). Plant, Cell & Environment 37 : 2553-76.